#work_align_tally_data-Brn1_genome-cat_printed.md
Table of contents
Printed
❯ #UPDATE
❯ # 2023-0715-0716: fastqs are now compressed, and symlinked/renamed files are
❯ #+ now stored in subdirectory sym/, e.g.,
❯ p_sym="${p_data}/sym"
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802"
❯ cd "${p_data}" || echo "cd'ing failed; check on this..."
❯ ls -lhaFG "${p_sym}"
total 1.3M
drwxrws--- 2 kalavatt 2.0K Jul 15 09:18 ./
drwxrws--- 5 kalavatt 1.8K Jul 16 06:28 ../
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175367.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175369.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175371.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175373.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175389.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175391.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175393.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_msn2_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200048.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200046.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175383.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175385.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175387.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200052.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175375.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175377.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175379.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175381.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Msn2_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200050.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175395.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175397.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175399.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200054.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175368.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175370.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175372.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175374.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175390.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175392.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175394.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_msn2_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200049.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200047.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175384.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175386.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175388.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200053.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175376.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175378.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175380.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175382.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Msn2_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200051.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175396.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175398.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175400.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200055.fastq.gz
❯ #NOTE
❯ # For more details on the symlinking/renaming process, see
❯ #+ 2023_rDNA/results/2023-0228_work_fastqs_download/work_download-data.mdPrinted
❯ grabnode
--------------------------------------------------------------
** Please review options as the order has changed **
- memory is requested first
- CPU selections will be adjusted based on memory request
--------------------------------------------------------------
How much memory (GB) will you need?
Enter a value from 1 to 683 [20]: 20
How many cores (CPUs) would you like to grab on the node?
enter a value between 1 and 36 [36]: 8
Please enter the max number of days you would like to grab this node: [1-7] 1
Do you need a GPU ? [y/N]N
You have requested 8 CPUs on this node/server for 1 days or until you type exit.
WARNING: If you exit this shell before your jobs are finished, your jobs
on this node/server will be terminated. Please use sbatch for larger jobs.
Shared PI folders can be found in: /fh/fast, /fh/scratch and /fh/secure.
Requesting Queue: campus-new cores: 8 memory: 20 gpu: NONE
srun: job 24831181 queued and waiting for resources
srun: job 24831181 has been allocated resources
❯ ml SAMtools/1.16.1-GCC-11.2.0 Bowtie2/2.4.4-GCC-11.2.0
❯ which bowtie2
/app/software/Bowtie2/2.4.4-GCC-11.2.0/bin/bowtie2
❯ # Set up work directory, directories for processed data
❯ d_work="${HOME}/tsukiyamalab/Kris/2023_rDNA/results" # cd "${d_work}"
❯ [[ ! -d "${d_work}/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out" ]] && \
> mkdir -p "${d_work}/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out"
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria'
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out'
❯ [[ ! -d "${d_work}/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out" ]] && \
> mkdir -p "${d_work}/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out"
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams'
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out'
❯ # Go to work directory
❯ cd "${d_work}" && pwd
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results
❯ # Initialize variables needed for alignment, etc.
❯ threads="${SLURM_CPUS_ON_NODE}" # echo "${threads}"
❯ d_genome="${HOME}/tsukiyamalab/Kris/genomes/combined_SC_SP" # ., "${d_genome}"
❯ f_genome="${d_genome}/fasta/combined_SC_SP.fa" # ., "${f_genome}"
❯ f_indices="${d_genome}/bowtie2/$(basename "${f_genome}" .fa)" # ., "${f_indices}"*
❯ err_out="${d_work}/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out" # ls -lhaFG "${err_out}"
❯ d_bams="$(dirname ${err_out})" # ls -lhaFG "${d_bams}"
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym" # ., "${p_data}"
❯ typeset -a fastqs=(
> "${p_data}/Ch_log_WT_Brn1_rep1.fastq.gz"
> "${p_data}/Ch_log_WT_Brn1_rep2.fastq.gz"
> "${p_data}/Ch_log_WT_Brn1_rep3.fastq.gz"
> "${p_data}/Ch_log_WT_Brn1_repM.fastq.gz"
> "${p_data}/Ch_Q_WT_Brn1_rep1.fastq.gz"
> "${p_data}/Ch_Q_WT_Brn1_rep2.fastq.gz"
> "${p_data}/Ch_Q_WT_Brn1_rep3.fastq.gz"
> "${p_data}/Ch_Q_WT_Brn1_repM.fastq.gz"
> "${p_data}/in_log_WT_Brn1_rep1.fastq.gz"
> "${p_data}/in_log_WT_Brn1_rep2.fastq.gz"
> "${p_data}/in_log_WT_Brn1_rep3.fastq.gz"
> "${p_data}/in_log_WT_Brn1_repM.fastq.gz"
> "${p_data}/in_Q_WT_Brn1_rep1.fastq.gz"
> "${p_data}/in_Q_WT_Brn1_rep2.fastq.gz"
> "${p_data}/in_Q_WT_Brn1_rep3.fastq.gz"
> "${p_data}/in_Q_WT_Brn1_repM.fastq.gz"
> )
❯ run_check=TRUE
❯ [[ "${run_check}" == TRUE ]] &&
> {
> echo '### echo "${threads}" ###'
> echo "${threads}"
> echo ""
>
> echo '### ls -lhaFG "${d_genome}" ###'
> ls -lhaFG "${d_genome}"
> echo ""
>
> echo '### ls -lhaFG "${f_genome}" ###'
> ls -lhaFG "${f_genome}"
> echo ""
>
> echo '### ls -lhaFG "${f_indices}"* ###'
> ls -lhaFG "${f_indices}"*
> echo ""
>
> echo '### ls -lhaFG "${err_out}" ###'
> ls -lhaFG "${err_out}"
> echo ""
>
> echo '### ls -lhaFG "${d_bams}" ###'
> ls -lhaFG "${d_bams}"
> echo ""
>
> echo '### ls -lhaFG "${p_data}" ###'
> ls -lhaFG "${p_data}"
> echo ""
>
> echo '### for i in "${fastqs[@]}"; do ls -lhaFG "${i}"; done ###'
> for i in "${fastqs[@]}"; do ls -lhaFG "${i}"; done
>
> echo '### for i in "${atria[@]}"; do echo "${i}"; done ###'
> for i in "${atria[@]}"; do echo "${i}"; done
> }
### echo "${threads}" ###
8
### ls -lhaFG "${scratch} ###
total 512
drwxrws--- 2 root 0 Jul 13 10:01 ./
drwxr-xr-x 250 root 248 Jul 5 07:00 ../
### ls -lhaFG "${d_genome}" ###
total 184K
drwxrwx--- 5 kalavatt 70 May 29 11:47 ./
drwxrwx--- 14 kalavatt 537 Jul 11 15:19 ../
drwxrwx--- 2 kalavatt 322 May 29 11:59 bowtie2/
drwxrwx--- 2 kalavatt 242 May 29 11:48 fasta/
drwxrwx--- 2 kalavatt 174 May 29 11:46 gff3/
### ls -lhaFG "${f_genome}" ###
-rw-rw---- 1 kalavatt 25M May 29 11:47 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/fasta/combined_SC_SP.fa
### ls -lhaFG "${f_indices}"* ###
-rw-rw---- 1 kalavatt 12M May 29 11:59 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.1.bt2
-rw-rw---- 1 kalavatt 6.0M May 29 11:59 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.2.bt2
-rw-rw---- 1 kalavatt 269 May 29 11:59 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.3.bt2
-rw-rw---- 1 kalavatt 6.0M May 29 11:59 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.4.bt2
-rw-rw---- 1 kalavatt 12M May 29 12:00 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.rev.1.bt2
-rw-rw---- 1 kalavatt 6.0M May 29 12:00 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.rev.2.bt2
-rw-rw---- 1 kalavatt 23 May 29 11:59 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.stderr.txt
-rw-rw---- 1 kalavatt 13K May 29 12:00 /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP.stdout.txt
### ls -lhaFG "${err_out}" ###
total 72K
drwxrws--- 2 kalavatt 0 Jul 16 06:43 ./
drwxrws--- 3 kalavatt 25 Jul 16 06:43 ../
### ls -lhaFG "${d_bams}" ###
total 112K
drwxrws--- 3 kalavatt 25 Jul 16 06:43 ./
drwxrws--- 4 kalavatt 363 Jul 16 07:11 ../
drwxrws--- 2 kalavatt 0 Jul 16 06:43 err_out/
### ls -lhaFG "${p_data}" ###
total 1.3M
drwxrws--- 2 kalavatt 2.0K Jul 15 09:18 ./
drwxrws--- 5 kalavatt 1.8K Jul 16 06:28 ../
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175367.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175369.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175371.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175373.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175389.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175391.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_log_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175393.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_msn2_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200048.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200046.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175383.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175385.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175387.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_SMC4-off_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200052.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175375.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175377.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175379.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175381.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Msn2_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200050.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175395.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175397.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175399.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 Ch_Q_WT_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200054.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175368.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175370.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175372.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175374.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175390.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175392.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_log_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175394.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_msn2_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200049.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200047.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175384.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175386.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175388.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_SMC4-off_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200053.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175376.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175378.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175380.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175382.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Msn2_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200051.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175396.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175398.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Rpb3_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175400.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 in_Q_WT_Ser2-phos_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR8200055.fastq.gz
### for i in "${fastqs[@]}"; do ls -lhaFG "${i}"; done ###
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175367.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175369.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175371.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175373.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175375.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175377.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175379.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175381.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175368.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175370.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175372.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175374.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep1.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175376.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep2.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175378.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep3.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175380.fastq.gz
lrwxrwxrwx 1 kalavatt 83 Jul 15 09:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_repM.fastq.gz -> /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/data/PRJNA471802/SRR7175382.fastq.gz
### for i in "${atria[@]}"; do echo "${i}"; done ###
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep2.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep3.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_repM.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep1.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep2.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep3.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_repM.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep1.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep2.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep3.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_repM.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep1.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep2.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep3.atria.fastq.gz
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.fastq.gzPrinted
❯ # Run print tests to check that the commands are correct/reasonable
❯ print_test=TRUE
❯ [[ "${print_test}" == TRUE ]] &&
> {
> for i in "${fastqs[@]}"; do
> echo """
> \"\${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria\" \\
> -t \"${threads}\" \\
> -r \"${i}\" \\
> -o \"${p_atria}\" \\
> --length-range 35:500
> """
> done
> }
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep1.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep2.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep3.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_repM.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep1.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep2.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep3.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_repM.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep1.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep2.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep3.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_repM.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep1.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep2.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep3.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
"${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
-t "8" \
-r "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_repM.fastq.gz" \
-o "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria" \
--length-range 35:500
❯ # If things look good, then run the calls to atria (the program for trimming)
❯ run=TRUE
❯ [[ "${run}" == "${run}" ]] &&
> {
> # Initialize environment for atria's dependencies
> [[ "${CONDA_DEFAULT_ENV}" != "atria_env" ]] && source activate atria_env
>
> for i in "${fastqs[@]}"; do
> "${HOME}/tsukiyamalab/kalavatt/2023_rDNA/src/Atria/app-3.2.2/bin/atria" \
> -t "${threads}" \
> -r "${i}" \
> -o "${p_atria}" \
> --length-range 35:500
> done
> }
┌ Info: ATRIA VERSIONS
│ atria = "v3.2.2"
└ julia = "v1.8.5"
┌ Info: ATRIA ARGUMENTS
└ command = `-t 8 -r /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep1.fastq.gz -o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria --length-range 35:500`
┌ Info: ATRIA OUTPUT FILES
└ read = "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.fastq.gz"
┌ Info: ATRIA TRIMMERS AND FILTERS
│ tail_polyG_trimming = false
│ tail_polyT_trimming = false
│ tail_polyA_trimming = false
│ tail_polyC_trimming = false
│ adapter_trimming = true
│ consensus_calling = false
│ hard_clip_3_end = false
│ hard_clip_5_end = false
│ quality_trimming = true
│ tail_N_trimming = true
│ max_N_filtering = true
│ length_filtering = true
└ complexity_filtering = false
[ Info: Cycle 1: read 388237/388237 pairs; wrote 368390/368390; (copied 0/0)
[ Info: Cycle 2: read 385683/773920 pairs; wrote 365573/733963; (copied 0/0)
[ Info: Cycle 3: read 382096/1156016 pairs; wrote 360165/1094128; (copied 0/0)
[ Info: Cycle 4: read 377016/1533032 pairs; wrote 350980/1445108; (copied 0/0)
[ Info: Cycle 5: read 377016/1910048 pairs; wrote 355116/1800224; (copied 0/0)
... (see logs)
┌ Info: ATRIA COMPLETE
└ read = "/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.fastq.gz"
❯ # Move atria logs to atria/err_out/
❯ [[ $(find "${p_atria}" -type f \( -name "*.log" -o -name "*.json" \) | wc -l) -gt 0 ]] && \
> mv ${p_atria}/*.{log,json} "${p_atria}/err_out"
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rD
NA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep1.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep2.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep2.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep3.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep3.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_repM.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_repM.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep1.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep1.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep2.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep2.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep3.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep3.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_repM.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_repM.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep1.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep1.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep2.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rD
NA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep2.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep3.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rD
NA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep3.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_repM.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rD
NA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_repM.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep1.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA
/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep1.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep2.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA
/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep2.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep3.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA
/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep3.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.log' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA
/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_repM.atria.log'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep1.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep2.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep2.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep3.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_rep3.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_repM.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_log_WT_Brn1_repM.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep1.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep1.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep2.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep2.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep3.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_rep3.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_repM.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/Ch_Q_WT_Brn1_repM.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep1.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep1.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep2.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep2.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep3.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_rep3.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_repM.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/20
23_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_log_WT_Brn1_repM.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep1.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep1.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep2.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep2.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep3.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_rep3.atria.log.json'
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.log.json' -> '/home/kalavatt/tsukiyamalab/Kris/2023
_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/err_out/in_Q_WT_Brn1_repM.atria.log.json'
❯ # Check that "${atria[@]}" array elements exist/are recognized by the system
❯ run_check=TRUE
❯ [[ "${run_check}" == TRUE ]] &&
> {
> echo '### for i in "${atria[@]}"; do ls -lhaFG "${i}"; done ###'
> for i in "${atria[@]}"; do ls -lhaFG "${i}"; done
> }
### for i in "${atria[@]}"; do ls -lhaFG "${i}"; done ###
-rw-rw---- 1 kalavatt 198M Jul 16 15:40 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.fastq.gz
-rw-rw---- 1 kalavatt 959M Jul 16 15:41 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep2.atria.fastq.gz
-rw-rw---- 1 kalavatt 268M Jul 16 15:41 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep3.atria.fastq.gz
-rw-rw---- 1 kalavatt 1.4G Jul 16 15:42 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_repM.atria.fastq.gz
-rw-rw---- 1 kalavatt 240M Jul 16 15:43 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep1.atria.fastq.gz
-rw-rw---- 1 kalavatt 215M Jul 16 15:43 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep2.atria.fastq.gz
-rw-rw---- 1 kalavatt 303M Jul 16 15:43 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep3.atria.fastq.gz
-rw-rw---- 1 kalavatt 760M Jul 16 15:44 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_repM.atria.fastq.gz
-rw-rw---- 1 kalavatt 491M Jul 16 15:45 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep1.atria.fastq.gz
-rw-rw---- 1 kalavatt 391M Jul 16 15:45 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep2.atria.fastq.gz
-rw-rw---- 1 kalavatt 284M Jul 16 15:46 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep3.atria.fastq.gz
-rw-rw---- 1 kalavatt 1.2G Jul 16 15:47 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_repM.atria.fastq.gz
-rw-rw---- 1 kalavatt 364M Jul 16 15:47 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep1.atria.fastq.gz
-rw-rw---- 1 kalavatt 421M Jul 16 15:48 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep2.atria.fastq.gz
-rw-rw---- 1 kalavatt 358M Jul 16 15:48 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep3.atria.fastq.gz
-rw-rw---- 1 kalavatt 1.2G Jul 16 15:49 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.fastq.gzPrinted
❯ # Run print tests to check that the commands are correct/reasonable
❯ print_test=TRUE
❯ [[ "${print_test}" == TRUE ]] &&
> {
> for i in "${atria[@]}"; do
> # i="${atria[0]}" # ., "${i}"
> in_fastq="${i}" # ., "${in_fastq}"
> out_bam="${d_bams}/$(basename "${in_fastq}" .fastq.gz).bam" # echo "${out_bam}"
>
> echo """
> # ---------------------------------------------------------
> # Align fastqs trimmed with atria; sort resulting bams
> {
> bowtie2 \\
> -p ${threads} \\
> -x ${f_indices} \\
> --end-to-end \\
> --very-fast \\
> -U ${i} \\
> | samtools sort \\
> -@ ${threads} \\
> -T ${scratch} \\
> -O bam \\
> -o ${out_bam}
> } \\
> > >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt) \\
> 2> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt)
>
> # Index the sorted bams
> if [[ -f ${out_bam} ]]; then
> samtools index \\
> -@ ${threads} \\
> ${out_bam} \\
> > >(tee -a ${err_out}/$(basename ${out_bam} .bam).samtools-index.stdout.txt) \\
> 2> >(tee -a ${err_out}/$(basename ${out_bam} .bam).samtools-index.stderr.txt)
> fi
> """
> done
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep1.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep2.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_rep3.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_log_WT_Brn1_repM.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep1.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep2.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_rep3.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/Ch_Q_WT_Brn1_repM.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep1.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep2.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_rep3.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_log_WT_Brn1_repM.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep1.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep2.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_rep3.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.atria.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align fastqs trimmed with atria; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--end-to-end \
--very-fast \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/atria/in_Q_WT_Brn1_repM.atria.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.atria.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.atria.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.atria.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.atria.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.atria.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.atria.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.atria.samtools-index.stderr.txt)
fi
❯ run=TRUE
❯ [[ "${run}" == TRUE ]] &&
> {
> for i in "${atria[@]}"; do
> # i="${atria[0]}" # echo "${i}"
> in_fastq="${i}" # ., "${in_fastq}"
> out_bam="${d_bams}/$(basename "${in_fastq}" .fastq.gz).bam" # echo "${out_bam}"
>
> echo "#### Aligning, sorting, indexing $(basename ${in_fastq}) ####"
> # Align fastqs trimmed with atria; sort resulting bams
> {
> bowtie2 \
> -p "${threads}" \
> --end-to-end \
> --very-fast \
> -x "${f_indices}" \
> -U "${in_fastq}" \
> | samtools sort \
> -@ "${threads}" \
> -T "${scratch}" \
> -O "bam" \
> -o "${out_bam}"
> } \
> > "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt" \
> 2> "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt"
>
> # Index the sorted bams
> if [[ -f "${out_bam}" ]]; then
> samtools index \
> -@ "${threads}" \
> "${out_bam}" \
> > >(tee -a "${err_out}/$(basename "${out_bam}" .bam).samtools-index.stdout.txt") \
> 2> >(tee -a "${err_out}/$(basename "${out_bam}" .bam).samtools-index.stderr.txt")
> fi
>
> if [[ -f "${out_bam}" && -f "${out_bam}.bai" ]]; then
> echo "#DONE"
> else
> echo "#PROBLEM"
> fi
> echo ""
> done
> }
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep1.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep2.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep3.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_repM.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep1.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep2.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep3.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_repM.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep1.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep2.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep3.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_repM.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep1.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep2.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep3.atria.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_repM.atria.fastq.gz ####
#DONEPrinted
❯ # Align un-trimmed fastqs --------------------------------
❯ # Run print tests to check that the commands are correct/reasonable
❯ print_test=TRUE
❯ [[ "${print_test}" == TRUE ]] &&
> {
> for i in "${fastqs[@]}"; do
> # i="${fastqs[0]}" # ., "${i}"
> in_fastq="${i}" # ., "${in_fastq}"
> out_bam="${d_bams}/$(basename "${in_fastq}" .fastq.gz).bam" # echo "${out_bam}"
>
> echo """
> # ---------------------------------------------------------
> # Align untrimmed fastqs; sort resulting bams
> {
> bowtie2 \\
> -p ${threads} \\
> -x ${f_indices} \\
> --very-sensitive-local \\
> -U ${i} \\
> | samtools sort \\
> -@ ${threads} \\
> -T ${scratch} \\
> -O bam \\
> -o ${out_bam}
> } \\
> > >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt) \\
> 2> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt)
>
> # Index the sorted bams
> if [[ -f ${out_bam} ]]; then
> samtools index \\
> -@ ${threads} \\
> ${out_bam} \\
> > >(tee -a ${err_out}/$(basename ${out_bam} .bam).samtools-index.stdout.txt) \\
> 2> >(tee -a ${err_out}/$(basename ${out_bam} .bam).samtools-index.stderr.txt)
> fi
> """
> done
> }
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep1.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep1.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep2.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep2.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_rep3.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_rep3.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_log_WT_Brn1_repM.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_log_WT_Brn1_repM.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep1.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep1.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep2.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep2.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_rep3.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_rep3.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/Ch_Q_WT_Brn1_repM.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/Ch_Q_WT_Brn1_repM.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep1.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep1.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep2.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep2.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_rep3.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_rep3.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_log_WT_Brn1_repM.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_log_WT_Brn1_repM.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep1.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep1.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep2.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep2.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_rep3.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_rep3.samtools-index.stderr.txt)
fi
# ---------------------------------------------------------
# Align untrimmed fastqs; sort resulting bams
{
bowtie2 \
-p 8 \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/combined_SC_SP/bowtie2/combined_SC_SP \
--very-sensitive-local \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/sym/in_Q_WT_Brn1_repM.fastq.gz \
| samtools sort \
-@ 8 \
-T /fh/scratch/delete30/tsukiyama_t \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.bam
} \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.bowtie2_samtools-sort.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.bowtie2_samtools-sort.stderr.txt)
# Index the sorted bams
if [[ -f /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.bam ]]; then
samtools index \
-@ 8 \
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.samtools-index.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/err_out/in_Q_WT_Brn1_repM.samtools-index.stderr.txt)
fi
❯ run=TRUE
❯ [[ "${run}" == TRUE ]] &&
> {
> for i in "${fastqs[@]}"; do
> # i="${fastqs[0]}" # echo "${i}"
> in_fastq="${i}" # ., "${in_fastq}"
> out_bam="${d_bams}/$(basename "${in_fastq}" .fastq.gz).bam" # echo "${out_bam}"
>
> # [[ -f "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt" ]] && \
> # rm "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt"
> #
> # [[ -f "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt" ]] && \
> # rm "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt"
>
> echo "#### Aligning, sorting, indexing $(basename ${in_fastq}) ####"
> # Align untrimmed fastqs; sort resulting bams
> {
> bowtie2 \
> -p "${threads}" \
> --very-sensitive-local \
> -x "${f_indices}" \
> -U "${in_fastq}" \
> | samtools sort \
> -@ "${threads}" \
> -T "${scratch}" \
> -O "bam" \
> -o "${out_bam}"
> } \
> > "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stdout.txt" \
> 2> "${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort.stderr.txt"
>
> # Index the sorted bams
> if [[ -f "${out_bam}" ]]; then
> samtools index \
> -@ "${threads}" \
> "${out_bam}" \
> > >(tee -a "${err_out}/$(basename "${out_bam}" .bam).samtools-index.stdout.txt") \
> 2> >(tee -a "${err_out}/$(basename "${out_bam}" .bam).samtools-index.stderr.txt")
> fi
>
> if [[ -f "${out_bam}" && -f "${out_bam}.bai" ]]; then
> echo "#DONE"
> else
> echo "#PROBLEM"
> fi
> echo ""
> done
> }
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep1.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep2.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_rep3.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_log_WT_Brn1_repM.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep1.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep2.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_rep3.fastq.gz ####
#DONE
#### Aligning, sorting, indexing Ch_Q_WT_Brn1_repM.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep1.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep2.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_rep3.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_log_WT_Brn1_repM.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep1.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep2.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_rep3.fastq.gz ####
#DONE
#### Aligning, sorting, indexing in_Q_WT_Brn1_repM.fastq.gz ####
#DONEPrinted
❯ check_dependency() {
> what="""
> check_dependency()
> ------------------
> Check if a program is available in the current environment
>
> :param 1: program to check <chr>
>
> #DONE Check that params are not empty
> #TODO Check that params are appropriate formats/strings
> #TODO Print to stderr
> """
>
> warning="""
> WARNING: param 1 is empty; stopping the function
> """
>
> [[ -z "${1}" ]] &&
> {
> echo "${warning}"
> echo "${what}"
>
> return 1
> }
>
> command -v "${1}" &>/dev/null ||
> {
> echo "Warning: ${1} not found. Install or load ${1}. Stopping the function."
> return 1
> }
> }
❯ calculate_run_time() {
> what="""
> calculate_run_time()
> --------------------
> Calculate run time for chunk of code
>
> :param 1: start time in \$(date +%s) format
> :param 2: end time in \$(date +%s) format
> :param 3: message to be displayed when printing the run time <chr>
>
> #DONE Check that params are not empty
> #TODO Check that params are appropriate formats/strings
> #TODO Print to stderr
> """
>
> warning="""
> WARNING: param(s) 1, 2, and/or 3 is/are empty; stopping the function
> """
>
> [[ -z "${1}" || -z "${2}" || -z "${3}" ]] &&
> {
> echo "${warning}"
> echo "${what}"
>
> return 1
> }
>
> run_time="$(echo "${2}" - "${1}" | bc -l)"
>
> echo ""
> echo "${3}"
> printf 'Run time: %dh:%dm:%ds\n' \
> $(( run_time/3600 )) \
> $(( run_time%3600/60 )) \
> $(( run_time%60 ))
> echo ""
> }
❯ display_spinning_icon() {
> what="""
> display_spinning_icon()
> -----------------------
> Display \"spinning icon\" while a background process runs
>
> :param 1: PID of the last program the shell ran in the background <pos int>
> :param 2: message to be displayed next to the spinning icon <chr>
>
> #DONE Check that params are not empty
> #TODO Check that params are appropriate formats/strings
> #TODO Print to stderr
> """
>
> warning="""
> WARNING: param(s) 1 and/or 2 is/are empty; stopping the function
> """
>
> [[ -z "${1}" || -z "${2}" ]] &&
> {
> echo "${warning}"
> echo "${what}"
>
> return 1
> }
>
> spin="/|\\–"
> i=0
> while kill -0 "${1}" 2> /dev/null; do
> i=$(( (i + 1) % 4 ))
> printf "\r${spin:$i:1} %s" "${2}"
> sleep .15
> done
> }
❯ list_tally_flags() {
> what="""
> list_tally_flags()
> ------------------
> List and tally flags in a bam infile; function acts on a bam infile to
> perform piped commands (samtools view, cut, sort, uniq -c, sort -nr) that
> list and tally flags; function writes the results to a txt outfile, the
> name of which is derived from the infile
>
> :param 1: name of bam infile, including path (chr)
>
> #DONE Check that param string is not empty
> #DONE Check that param file exists
> #DONE Check that dependency is present
> #TODO Check that params are appropriate formats/strings
> #TODO Print to stderr
> """
>
> warning_param="""
> WARNING: param 1 is empty; stopping the function
> """
>
> warning_file="""
> WARNING: param 1 file not found; stopping the function
> """
>
> warning_depend="""
> WARNING: One or more dependencies not found; stopping the function
> """
>
> [[ -z "${1}" ]] &&
> {
> echo "${warning_param}"
> echo "${what}"
> return 1
> }
>
> [[ -f "${1}" ]] ||
> {
> echo "${warning_file}"
> echo "${what}"
> return 1
> }
>
> check_dependency samtools \
> && check_dependency sort \
> && check_dependency uniq \
> && check_dependency display_spinning_icon \
> && check_dependency calculate_run_time
> [[ $? -gt 0 ]] &&
> {
> echo "${warning_depend}"
> return 1
> }
>
> start="$(date +%s)"
>
> samtools view "${1}" \
> | cut -f 2 \
> | sort \
> | uniq -c \
> | sort -nr \
> > "${1/.bam/.flags.txt}" &
> display_spinning_icon $! \
> "Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on $(basename "${1}")... "
>
> end="$(date +%s)"
> echo ""
> calculate_run_time "${start}" "${end}" \
> "List and tally flags in $(basename "${1}")."
> }
❯ list_tally_MAPQs() {
> what="""
> list_tally_MAPQs()
> ------------------
> List and tally MAPQ scores in a bam infile; function acts on a bam infile
> to perform piped commands (samtools view, cut, sort, uniq -c, sort -nr)
> that list and tally MAPQ scores; function writes the results to a txt
> outfile, the name of which is derived from the infile
>
> :param 1: name of bam infile, including path (chr)
>
> #DONE Check that param string is not empty
> #DONE Check that param file exists
> #DONE Check that dependency is present
> #TODO Check that params are appropriate formats/strings
> #TODO Print to stderr
> """
>
> warning_param="""
> WARNING: param 1 is empty; stopping the function
> """
>
> warning_file="""
> WARNING: param 1 file not found; stopping the function
> """
>
> warning_depend="""
> WARNING: One or more dependencies not found; stopping the function
> """
>
> [[ -z "${1}" ]] &&
> {
> echo "${warning_param}"
> echo "${what}"
> return 1
> }
>
> [[ -f "${1}" ]] ||
> {
> echo "${warning_file}"
> echo "${what}"
> return 1
> }
>
> check_dependency samtools \
> && check_dependency sort \
> && check_dependency uniq \
> && check_dependency display_spinning_icon \
> && check_dependency calculate_run_time
> [[ $? -gt 0 ]] &&
> {
> echo "${warning_depend}"
> return 1
> }
>
> start="$(date +%s)"
>
> samtools view "${1}" \
> | cut -f 5 \
> | sort \
> | uniq -c \
> | sort -nr \
> > "${1/.bam/.MAPQs.txt}" &
> display_spinning_icon $! \
> "Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on $(basename "${1}")... "
>
> end="$(date +%s)"
> echo ""
> calculate_run_time "${start}" "${end}" \
> "List and tally MAPQ scores in $(basename "${1}")."
> }Printed
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams"
❯ unset bams
❯ typeset -a bams=(
> "${p_data}/Ch_log_WT_Brn1_rep1.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep1.bam"
> "${p_data}/Ch_log_WT_Brn1_rep2.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep2.bam"
> "${p_data}/Ch_log_WT_Brn1_rep3.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep3.bam"
> "${p_data}/Ch_log_WT_Brn1_repM.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_repM.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep1.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep1.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep2.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep2.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep3.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep3.bam"
> "${p_data}/Ch_Q_WT_Brn1_repM.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_repM.bam"
> "${p_data}/in_log_WT_Brn1_rep1.atria.bam"
> "${p_data}/in_log_WT_Brn1_rep1.bam"
> "${p_data}/in_log_WT_Brn1_rep2.atria.bam"
> "${p_data}/in_log_WT_Brn1_rep2.bam"
> "${p_data}/in_log_WT_Brn1_rep3.atria.bam"
> "${p_data}/in_log_WT_Brn1_rep3.bam"
> "${p_data}/in_log_WT_Brn1_repM.atria.bam"
> "${p_data}/in_log_WT_Brn1_repM.bam"
> "${p_data}/in_Q_WT_Brn1_rep1.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep1.bam"
> "${p_data}/in_Q_WT_Brn1_rep2.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep2.bam"
> "${p_data}/in_Q_WT_Brn1_rep3.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep3.bam"
> "${p_data}/in_Q_WT_Brn1_repM.atria.bam"
> "${p_data}/in_Q_WT_Brn1_repM.bam"
> )
❯ run_check=TRUE
❯ [[ "${run_check}" == TRUE ]] &&
> {
> for i in "${bams[@]}"; do ls -lhaFG "${i}"; done
> }
-rw-rw---- 1 kalavatt 132M Jul 16 15:59 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 142M Jul 16 14:29 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.bam
-rw-rw---- 1 kalavatt 585M Jul 16 20:31 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 635M Jul 16 14:33 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.bam
-rw-rw---- 1 kalavatt 180M Jul 16 20:31 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 196M Jul 16 14:34 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.bam
-rw-rw---- 1 kalavatt 863M Jul 16 21:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 940M Jul 16 14:39 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.bam
-rw-rw---- 1 kalavatt 172M Jul 16 21:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 181M Jul 16 14:39 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.bam
-rw-rw---- 1 kalavatt 150M Jul 16 21:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 159M Jul 16 14:40 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.bam
-rw-rw---- 1 kalavatt 209M Jul 16 21:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 230M Jul 16 14:41 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.bam
-rw-rw---- 1 kalavatt 506M Jul 16 21:20 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 547M Jul 16 14:43 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.bam
-rw-rw---- 1 kalavatt 348M Jul 16 21:21 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 385M Jul 16 14:45 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.bam
-rw-rw---- 1 kalavatt 279M Jul 16 21:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 309M Jul 16 14:46 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.bam
-rw-rw---- 1 kalavatt 199M Jul 16 21:23 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 216M Jul 16 14:47 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.bam
-rw-rw---- 1 kalavatt 781M Jul 16 22:20 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 865M Jul 16 14:52 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.bam
-rw-rw---- 1 kalavatt 257M Jul 16 22:21 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 284M Jul 16 14:53 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.bam
-rw-rw---- 1 kalavatt 294M Jul 16 22:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 325M Jul 16 14:54 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.bam
-rw-rw---- 1 kalavatt 249M Jul 16 22:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 266M Jul 16 14:55 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.bam
-rw-rw---- 1 kalavatt 756M Jul 16 22:50 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 832M Jul 16 15:00 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.bam
❯ for i in "${bams[@]}"; do
> # i="${bams[0]}" # echo "${i}"
> echo "#### $(basename ${i}) ####"
> list_tally_MAPQs "${i}"
> echo ""
> done
#### Ch_log_WT_Brn1_rep1.atria.bam ####
[1] 64378
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:7s
#### Ch_log_WT_Brn1_rep1.bam ####
[1] 64679
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep1.bam.
Run time: 0h:0m:7s
#### Ch_log_WT_Brn1_rep2.atria.bam ####
[1] 64866
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:32s
#### Ch_log_WT_Brn1_rep2.bam ####
[1] 66137
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep2.bam.
Run time: 0h:0m:33s
#### Ch_log_WT_Brn1_rep3.atria.bam ####
[1] 66684
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:10s
#### Ch_log_WT_Brn1_rep3.bam ####
[1] 67160
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_rep3.bam.
Run time: 0h:0m:11s
#### Ch_log_WT_Brn1_repM.atria.bam ####
[1] 67858
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:49s
#### Ch_log_WT_Brn1_repM.bam ####
[1] 69105
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_log_WT_Brn1_repM.bam.
Run time: 0h:0m:54s
#### Ch_Q_WT_Brn1_rep1.atria.bam ####
[1] 71317
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:9s
#### Ch_Q_WT_Brn1_rep1.bam ####
[1] 71669
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep1.bam.
Run time: 0h:0m:9s
#### Ch_Q_WT_Brn1_rep2.atria.bam ####
[1] 71867
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:9s
#### Ch_Q_WT_Brn1_rep2.bam ####
[1] 72049
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep2.bam.
Run time: 0h:0m:8s
#### Ch_Q_WT_Brn1_rep3.atria.bam ####
[1] 72213
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:10s
#### Ch_Q_WT_Brn1_rep3.bam ####
[1] 72771
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_rep3.bam.
Run time: 0h:0m:11s
#### Ch_Q_WT_Brn1_repM.atria.bam ####
[1] 73124
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:28s
#### Ch_Q_WT_Brn1_repM.bam ####
[1] 523
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in Ch_Q_WT_Brn1_repM.bam.
Run time: 0h:0m:27s
#### in_log_WT_Brn1_rep1.atria.bam ####
[1] 1786
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:16s
#### in_log_WT_Brn1_rep1.bam ####
[1] 2369
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep1.bam.
Run time: 0h:0m:18s
#### in_log_WT_Brn1_rep2.atria.bam ####
[1] 3124
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:13s
#### in_log_WT_Brn1_rep2.bam ####
[1] 4012
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep2.bam.
Run time: 0h:0m:15s
#### in_log_WT_Brn1_rep3.atria.bam ####
[1] 4285
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:9s
#### in_log_WT_Brn1_rep3.bam ####
[1] 4439
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_rep3.bam.
Run time: 0h:0m:11s
#### in_log_WT_Brn1_repM.atria.bam ####
[1] 4943
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:39s
#### in_log_WT_Brn1_repM.bam ####
[1] 6697
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_log_WT_Brn1_repM.bam.
Run time: 0h:0m:42s
#### in_Q_WT_Brn1_rep1.atria.bam ####
[1] 8825
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:12s
#### in_Q_WT_Brn1_rep1.bam ####
[1] 9127
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep1.bam.
Run time: 0h:0m:15s
#### in_Q_WT_Brn1_rep2.atria.bam ####
[1] 10057
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:15s
#### in_Q_WT_Brn1_rep2.bam ####
[1] 11168
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep2.bam.
Run time: 0h:0m:15s
#### in_Q_WT_Brn1_rep3.atria.bam ####
[1] 11680
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:12s
#### in_Q_WT_Brn1_rep3.bam ####
[1] 12098
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_rep3.bam.
Run time: 0h:0m:14s
#### in_Q_WT_Brn1_repM.atria.bam ####
[1] 13193
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:37s
#### in_Q_WT_Brn1_repM.bam ####
[1] 14570
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 5 | sort | uniq -c | sort -nr > "${1/.bam/.MAPQs.txt}"
List and tally MAPQ scores in in_Q_WT_Brn1_repM.bam.
Run time: 0h:0m:40sPrinted
❯ for i in "${bams[@]}"; do
> # i="${bams[0]}" # echo "${i}"
> echo "#### $(basename ${i}) ####"
> list_tally_flags "${i}"
> echo ""
> done
#### Ch_log_WT_Brn1_rep1.atria.bam ####
[1] 59460
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:10s
#### Ch_log_WT_Brn1_rep1.bam ####
[1] 59669
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep1.bam.
Run time: 0h:0m:9s
#### Ch_log_WT_Brn1_rep2.atria.bam ####
[1] 60287
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:43s
#### Ch_log_WT_Brn1_rep2.bam ####
[1] 62542
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep2.bam.
Run time: 0h:0m:48s
#### Ch_log_WT_Brn1_rep3.atria.bam ####
[1] 64344
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:13s
#### Ch_log_WT_Brn1_rep3.bam ####
[1] 64725
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_rep3.bam.
Run time: 0h:0m:14s
#### Ch_log_WT_Brn1_repM.atria.bam ####
[1] 66124
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_repM.atria.bam.
Run time: 0h:1m:17s
#### Ch_log_WT_Brn1_repM.bam ####
[1] 72459
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_log_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_log_WT_Brn1_repM.bam.
Run time: 0h:1m:11s
#### Ch_Q_WT_Brn1_rep1.atria.bam ####
[1] 3012
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:10s
#### Ch_Q_WT_Brn1_rep1.bam ####
[1] 3649
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep1.bam.
Run time: 0h:0m:11s
#### Ch_Q_WT_Brn1_rep2.atria.bam ####
[1] 4117
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:10s
#### Ch_Q_WT_Brn1_rep2.bam ####
[1] 4288
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep2.bam.
Run time: 0h:0m:10s
#### Ch_Q_WT_Brn1_rep3.atria.bam ####
[1] 4476
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:16s
#### Ch_Q_WT_Brn1_rep3.bam ####
[1] 5149
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_rep3.bam.
Run time: 0h:0m:16s
#### Ch_Q_WT_Brn1_repM.atria.bam ####
[1] 6287
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:32s
#### Ch_Q_WT_Brn1_repM.bam ####
[1] 7080
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Ch_Q_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Ch_Q_WT_Brn1_repM.bam.
Run time: 0h:0m:36s
#### in_log_WT_Brn1_rep1.atria.bam ####
[1] 8664
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:22s
#### in_log_WT_Brn1_rep1.bam ####
[1] 9160
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep1.bam.
Run time: 0h:0m:23s
#### in_log_WT_Brn1_rep2.atria.bam ####
[1] 10562
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:19s
#### in_log_WT_Brn1_rep2.bam ####
[1] 11122
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep2.bam.
Run time: 0h:0m:20s
#### in_log_WT_Brn1_rep3.atria.bam ####
[1] 12039
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:12s
#### in_log_WT_Brn1_rep3.bam ####
[1] 12451
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_rep3.bam.
Run time: 0h:0m:12s
#### in_log_WT_Brn1_repM.atria.bam ####
[1] 12688
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:43s
#### in_log_WT_Brn1_repM.bam ####
[1] 18115
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_log_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_log_WT_Brn1_repM.bam.
Run time: 0h:0m:45s
#### in_Q_WT_Brn1_rep1.atria.bam ####
[1] 19754
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep1.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep1.atria.bam.
Run time: 0h:0m:13s
#### in_Q_WT_Brn1_rep1.bam ####
[1] 20117
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep1.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep1.bam.
Run time: 0h:0m:13s
#### in_Q_WT_Brn1_rep2.atria.bam ####
[1] 20516
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep2.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep2.atria.bam.
Run time: 0h:0m:15s
#### in_Q_WT_Brn1_rep2.bam ####
[1] 21091
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep2.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep2.bam.
Run time: 0h:0m:16s
#### in_Q_WT_Brn1_rep3.atria.bam ####
[1] 21508
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep3.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep3.atria.bam.
Run time: 0h:0m:13s
#### in_Q_WT_Brn1_rep3.bam ####
[1] 21734
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_rep3.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_rep3.bam.
Run time: 0h:0m:14s
#### in_Q_WT_Brn1_repM.atria.bam ####
[1] 22211
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_repM.atria.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_repM.atria.bam.
Run time: 0h:0m:37s
#### in_Q_WT_Brn1_repM.bam ####
[1] 23287
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on in_Q_WT_Brn1_repM.bam... [1]+ Done
samtools view "${1}" | cut -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in in_Q_WT_Brn1_repM.bam.
Run time: 0h:0m:44s
❯ for i in "${bams[@]}"; do
> if [[ -f "${i/.bam/.flags.txt}" ]]; then
> echo "#### $(basename ${i}) ####"
> cat "${i/.bam/.flags.txt}"
> echo ""
> fi
> done
#### Ch_log_WT_Brn1_rep1.atria.bam ####
2880211 16
2872535 0
499911 4
#### Ch_log_WT_Brn1_rep1.bam ####
3040301 16
3017984 0
585178 4
#### Ch_log_WT_Brn1_rep2.atria.bam ####
13759369 0
13695345 16
2734535 4
#### Ch_log_WT_Brn1_rep2.bam ####
14450767 0
14447432 16
3176492 4
#### Ch_log_WT_Brn1_rep3.atria.bam ####
3933313 0
3918289 16
316828 4
#### Ch_log_WT_Brn1_rep3.bam ####
4177590 16
4176208 0
429674 4
#### Ch_log_WT_Brn1_repM.atria.bam ####
20568347 0
20490732 16
3551257 4
#### Ch_log_WT_Brn1_repM.bam ####
21661810 16
21648500 0
4191316 4
#### Ch_Q_WT_Brn1_rep1.atria.bam ####
2753517 0
2738599 16
1739181 4
#### Ch_Q_WT_Brn1_rep1.bam ####
2874061 0
2862832 16
1890825 4
#### Ch_Q_WT_Brn1_rep2.atria.bam ####
2713945 0
2707745 16
1066876 4
#### Ch_Q_WT_Brn1_rep2.bam ####
2846780 0
2843810 16
1190484 4
#### Ch_Q_WT_Brn1_rep3.atria.bam ####
4128527 0
4125918 16
612389 4
#### Ch_Q_WT_Brn1_rep3.bam ####
4442444 16
4437645 0
780519 4
#### Ch_Q_WT_Brn1_repM.atria.bam ####
9594496 0
9573809 16
3418392 4
#### Ch_Q_WT_Brn1_repM.bam ####
10156605 0
10150983 16
3861812 4
#### in_log_WT_Brn1_rep1.atria.bam ####
6779624 0
6769780 16
333904 4
#### in_log_WT_Brn1_rep1.bam ####
7355182 0
7350937 16
550871 4
#### in_log_WT_Brn1_rep2.atria.bam ####
5415076 0
5397393 16
236372 4
#### in_log_WT_Brn1_rep2.bam ####
5876887 0
5862547 16
405161 4
#### in_log_WT_Brn1_rep3.atria.bam ####
4033815 16
4033137 0
195541 4
#### in_log_WT_Brn1_rep3.bam ####
4309499 16
4305931 0
306893 4
#### in_log_WT_Brn1_repM.atria.bam ####
16227991 0
16200760 16
765891 4
#### in_log_WT_Brn1_repM.bam ####
17538461 0
17522551 16
1262896 4
#### in_Q_WT_Brn1_rep1.atria.bam ####
5055045 0
5044226 16
220686 4
#### in_Q_WT_Brn1_rep1.bam ####
5483653 0
5478220 16
370063 4
#### in_Q_WT_Brn1_rep2.atria.bam ####
5865241 0
5848241 16
217378 4
#### in_Q_WT_Brn1_rep2.bam ####
6351723 0
6342962 16
365205 4
#### in_Q_WT_Brn1_rep3.atria.bam ####
5097671 0
5086953 16
265277 4
#### in_Q_WT_Brn1_rep3.bam ####
5400769 0
5392613 16
367131 4
#### in_Q_WT_Brn1_repM.atria.bam ####
16017543 0
15979878 16
703297 4
#### in_Q_WT_Brn1_repM.bam ####
17235945 0
17214003 16
1102391 4
❯ for i in "${bams[@]}"; do
> if [[ -f "${i/.bam/.MAPQs.txt}" ]]; then
> echo "#### $(basename ${i}) ####"
> cat "${i/.bam/.MAPQs.txt}"
> echo ""
> fi
> done
#### Ch_log_WT_Brn1_rep1.atria.bam ####
2945073 42
2623328 1
518847 0
63857 40
22728 30
10515 39
10217 24
9207 32
8949 23
6278 37
6028 35
4683 36
3732 31
3068 3
3028 38
2447 8
2413 2
1598 34
1064 7
688 15
678 6
617 16
590 26
535 4
535 22
511 11
406 5
355 14
152 27
149 12
148 25
98 18
75 21
39 17
21 33
#### Ch_log_WT_Brn1_rep1.bam ####
3017395 44
2758358 1
595062 0
29139 42
25740 31
22044 37
19791 39
17535 11
16904 41
16764 38
16123 34
15319 40
14456 32
13845 33
10208 35
8198 36
6686 14
5281 25
4871 2
4842 28
4571 21
4002 22
3774 17
2851 18
2481 24
2293 9
2041 12
1764 16
1125 19
#### Ch_log_WT_Brn1_rep2.atria.bam ####
14002100 42
12579782 1
2826048 0
300446 40
106109 30
51017 39
50294 24
42217 23
42138 32
29795 35
29525 37
21726 36
18074 31
14773 3
13545 38
12122 8
10770 2
7806 34
4660 7
3175 15
3174 6
2835 22
2738 26
2721 16
2483 11
2295 4
2041 5
1655 14
756 27
708 12
666 25
411 18
335 21
193 17
116 33
#### Ch_log_WT_Brn1_rep2.bam ####
14325384 44
13227785 1
3222823 0
139813 42
121118 31
106859 37
97425 39
81467 41
80225 11
79924 38
78030 40
75369 34
67565 32
66338 33
47971 35
39465 36
30622 14
24762 25
22870 2
21809 21
20084 22
19636 28
17792 17
13323 18
12300 24
11040 9
9112 12
8303 16
5477 19
#### Ch_log_WT_Brn1_rep3.atria.bam ####
4860491 42
2695978 1
338356 0
123359 40
36526 30
14795 24
14210 39
13180 23
13128 32
9932 37
9491 35
6539 36
6056 31
4909 38
4134 3
3325 8
2853 34
2295 2
1526 7
975 15
926 26
900 6
803 16
746 22
656 11
561 4
521 5
462 14
205 27
192 12
144 25
115 18
71 21
43 17
27 33
#### Ch_log_WT_Brn1_rep3.bam ####
5062849 44
2874951 1
440782 0
52561 42
41543 31
30186 39
29532 37
29329 41
27474 40
24240 38
24072 34
20658 11
20595 33
19577 32
14879 35
12630 36
8487 14
6314 25
5872 21
5870 28
5586 2
5426 22
4850 17
3975 18
3418 24
2686 9
2172 12
1834 16
1124 19
#### Ch_log_WT_Brn1_repM.atria.bam ####
21807635 42
17899082 1
3683398 0
487693 40
165362 30
75660 39
75273 24
64525 32
64267 23
45954 37
45164 35
32967 36
27827 31
21885 3
21454 38
17921 8
15498 2
12208 34
7195 7
4832 6
4827 15
4194 16
4172 26
4114 22
3759 11
3350 4
3019 5
2385 14
1158 27
1076 12
949 25
628 18
459 21
283 17
163 33
#### Ch_log_WT_Brn1_repM.bam ####
22405451 44
18861127 1
4258614 0
221559 42
188407 31
158549 37
147380 39
127586 41
121070 38
120872 40
118354 11
115577 34
101638 32
100743 33
72996 35
60264 36
46007 14
36486 25
33136 2
32193 21
30348 28
29511 22
26301 17
20137 18
18191 24
16181 9
13399 12
11860 16
7689 19
#### Ch_Q_WT_Brn1_rep1.atria.bam ####
3685023 42
1749695 0
1616895 1
81918 40
27594 30
8835 23
8748 24
8408 32
6889 39
6003 35
5562 37
4992 31
3155 36
3038 38
2804 3
2140 8
2102 34
1562 2
1089 7
649 6
641 15
597 26
518 16
509 22
468 11
306 4
305 5
290 14
143 12
121 25
113 27
75 18
46 21
45 17
19 33
#### Ch_Q_WT_Brn1_rep1.bam ####
3814348 44
1895799 0
1686784 1
30200 31
28293 42
18435 41
15980 40
15572 39
14899 37
12912 33
12847 34
11867 38
11467 11
9762 32
8001 35
7321 36
5408 14
3719 22
3453 2
3273 28
3057 21
2890 17
2830 25
2423 18
2412 24
1581 9
971 12
768 16
446 19
#### Ch_Q_WT_Brn1_rep2.atria.bam ####
3348796 42
1900257 1
1075903 0
75405 40
24088 30
8905 24
8449 23
7436 32
6110 39
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4464 31
3018 36
2709 38
2484 3
2068 8
1844 34
1167 2
917 7
602 6
566 15
487 26
460 22
424 16
370 11
299 5
278 4
226 14
151 12
104 25
98 27
79 18
50 21
42 17
13 33
#### Ch_Q_WT_Brn1_rep2.bam ####
3481145 44
1988375 1
1196104 0
29767 42
26385 31
18293 41
14054 39
13749 37
13284 40
11355 34
11077 33
10777 38
10325 11
9221 32
7458 36
7239 35
4808 14
4072 28
3424 2
3223 25
3097 21
3011 22
2682 17
2211 18
2111 24
1551 9
1056 12
716 16
504 19
#### Ch_Q_WT_Brn1_rep3.atria.bam ####
5256157 42
2686308 1
635770 0
126865 40
39140 30
16327 24
14030 23
13605 39
13571 32
9939 35
9590 37
6740 36
6715 31
5449 38
4720 3
3880 2
3697 8
3159 34
1929 7
1300 6
1217 15
1077 16
1004 26
955 11
921 22
752 4
669 14
588 5
209 27
162 12
149 25
92 18
77 21
58 17
13 33
#### Ch_Q_WT_Brn1_rep3.bam ####
5540008 44
2892269 1
792488 0
64790 42
44453 31
35829 41
28370 40
28286 39
27757 37
24769 11
22852 34
22547 38
20278 33
19853 32
15468 36
15274 35
10938 14
9039 28
6068 22
6055 17
5760 25
5655 21
5596 2
4386 18
4165 24
2770 9
2048 12
1708 16
1129 19
#### Ch_Q_WT_Brn1_repM.atria.bam ####
12290058 42
6203473 1
3461395 0
284215 40
90822 30
34010 24
31325 23
29512 32
26544 39
21233 35
20208 37
16118 31
12895 36
11100 38
9957 3
7897 8
7117 34
6588 2
3889 7
2540 6
2449 15
2005 16
2002 26
1922 22
1827 11
1360 4
1200 14
1173 5
469 12
404 27
372 25
246 18
173 21
149 17
50 33
#### Ch_Q_WT_Brn1_repM.bam ####
12835510 44
6567349 1
3884286 0
122810 42
101090 31
72506 41
58024 39
57626 40
56437 37
47052 34
46719 11
45154 38
44204 33
38777 32
30546 35
30248 36
21081 14
16408 28
12767 22
12595 2
11873 25
11732 21
11702 17
8928 18
8699 24
6034 9
4076 12
3133 16
2034 19
#### in_log_WT_Brn1_rep1.atria.bam ####
10590105 42
2493180 1
351181 0
201739 40
76537 30
24065 24
22332 32
20440 23
16185 35
15150 39
13824 37
12460 31
7766 38
7398 36
5698 3
5310 34
4982 8
2728 7
2044 2
1841 6
1303 15
1148 16
1136 26
951 22
852 11
543 14
514 5
472 12
444 4
263 25
251 27
212 18
112 17
99 21
43 33
#### in_log_WT_Brn1_rep1.bam ####
11318170 44
2708880 1
557409 0
133091 42
83874 31
65984 41
46863 40
40740 39
34777 37
33892 34
32671 33
30516 38
27133 36
26087 32
22931 11
22804 35
12859 14
9926 28
7482 22
6710 21
6630 17
5961 24
5936 25
5462 18
4336 2
2330 9
1696 12
1156 16
684 19
#### in_log_WT_Brn1_rep2.atria.bam ####
8325296 42
2124441 1
250385 0
157054 40
59273 30
18644 24
17432 32
15871 23
12553 35
11497 39
10716 37
9740 31
5963 38
5746 36
4357 3
4134 34
3830 8
2133 7
1726 2
1472 6
946 15
884 26
842 16
775 22
734 11
433 14
427 5
400 12
390 4
195 25
190 27
157 18
91 21
81 17
33 33
#### in_log_WT_Brn1_rep2.bam ####
8901995 44
2308538 1
410638 0
104567 42
65476 31
52057 41
34581 40
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27097 37
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23185 38
21630 36
20223 32
18124 11
17068 35
10132 14
8505 28
5638 22
5291 17
5274 21
4707 24
4672 25
4338 18
3655 2
1921 9
1318 12
918 16
523 19
#### in_log_WT_Brn1_rep3.atria.bam ####
6347819 42
1383922 1
206733 0
168296 40
45490 30
14609 23
14291 24
13519 32
10166 35
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7849 31
5174 38
4857 36
4134 3
3405 34
3176 8
1769 7
1388 2
1092 6
967 15
797 16
765 26
615 11
586 22
394 14
351 5
305 4
210 12
132 27
118 18
100 25
50 21
44 17
15 33
#### in_log_WT_Brn1_rep3.bam ####
6725442 44
1479637 1
310826 0
66145 42
49972 31
39259 41
32714 40
28157 39
23644 37
21493 34
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20344 38
15347 36
15105 32
14601 35
14134 11
7805 14
5954 28
4924 22
4256 21
4092 17
3980 25
3641 24
3523 18
2999 2
1567 9
1128 12
798 16
446 19
#### in_log_WT_Brn1_repM.atria.bam ####
25263314 42
6001547 1
808323 0
527071 40
181300 30
57010 24
53361 32
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18940 38
18026 36
14241 3
12807 34
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3233 15
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2756 16
2259 22
2186 11
1369 14
1221 5
1165 4
1079 12
591 27
542 25
503 18
250 21
237 17
96 33
#### in_log_WT_Brn1_repM.bam ####
26945601 44
6497037 1
1278786 0
303835 42
199311 31
157301 41
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61370 32
55126 11
54358 35
30898 14
24383 28
18060 22
16210 21
15966 17
14614 25
14322 24
13381 18
10926 2
5832 9
4178 12
2839 16
1682 19
#### in_Q_WT_Brn1_rep1.atria.bam ####
7575923 42
2156379 1
236725 0
142143 40
57353 30
18051 24
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16731 39
15637 23
14602 35
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9703 31
9020 38
7813 36
5128 3
4982 34
4371 8
2100 2
2071 7
1414 6
1361 26
1156 15
1139 16
1004 22
800 11
593 14
545 5
438 4
399 12
272 27
246 25
178 18
95 17
90 21
38 33
#### in_Q_WT_Brn1_rep1.bam ####
8021559 44
2340529 1
375766 0
96324 42
62806 31
55935 40
47344 41
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36740 37
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32236 34
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24325 35
22149 32
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20417 36
10626 14
8251 22
7797 28
6771 21
6248 17
6245 25
5620 24
5341 18
4687 2
2430 9
1885 12
1238 16
758 19
#### in_Q_WT_Brn1_rep2.atria.bam ####
8374819 42
2948443 1
234612 0
157176 40
62526 30
19988 24
18202 32
16949 23
15424 39
14443 35
13600 37
10408 31
8157 38
7601 36
5198 3
4832 34
4503 8
2157 7
2066 2
1587 6
1176 26
1147 15
1111 16
1006 22
859 11
576 14
548 5
484 4
390 12
242 27
227 25
169 18
113 21
88 17
33 33
#### in_Q_WT_Brn1_rep2.bam ####
8895664 44
3195672 1
372196 0
103244 42
68319 31
51209 41
48861 40
42396 39
34991 37
31310 34
30963 38
27848 33
22707 32
22471 35
21323 11
21205 36
11271 14
8946 28
7653 22
6954 21
6629 17
6475 25
5422 18
5335 24
4585 2
2426 9
1864 12
1226 16
725 19
#### in_Q_WT_Brn1_rep3.atria.bam ####
8208677 42
1567566 1
281494 0
187892 40
59173 30
18455 23
18257 24
17781 32
13576 35
13428 39
12352 37
10305 31
6996 38
6323 36
5270 3
4637 34
4012 8
2475 2
2364 7
1365 6
1175 15
1064 26
1064 16
903 11
802 22
585 14
488 5
482 4
257 12
203 27
170 25
144 18
85 21
57 17
24 33
#### in_Q_WT_Brn1_rep3.bam ####
8610317 44
1661701 1
371212 0
80249 42
64518 31
48035 41
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30420 37
28838 34
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25983 38
19947 32
19888 11
19405 35
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10393 14
6682 28
6220 22
5365 17
5316 21
4626 24
4625 25
4349 18
3494 2
1924 9
1321 12
934 16
559 19
#### in_Q_WT_Brn1_repM.atria.bam ####
24159430 42
6672387 1
752871 0
487229 40
179054 30
56317 24
52937 32
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30411 31
23917 38
21786 36
15667 3
14416 34
12876 8
6551 2
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3444 15
3354 16
2830 22
2550 11
1725 14
1557 5
1412 4
1025 12
696 27
640 25
500 18
301 21
236 17
106 33
#### in_Q_WT_Brn1_repM.bam ####
25527419 44
7197955 1
1119197 0
279789 42
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146585 41
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66186 35
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60102 36
32262 14
23443 28
22129 22
19044 21
18280 17
17248 25
15580 24
15076 18
12830 2
6729 9
5040 12
3406 16
2025 19Printed
❯ calc_6f() { awk "BEGIN{ printf \"%.6f\n\", $* }"; }
❯ calc_2f() { awk "BEGIN{ printf \"%.2f\n\", $* }"; }
❯ tally_alignments() {
> local OPTIND opt type MAPQ file Mito
> while getopts "t:q:f:m:" opt; do
> case "${opt}" in
> t) type="${OPTARG}" ;;
> q) MAPQ="${OPTARG}" ;;
> f) file="${OPTARG}" ;;
> m) Mito="${OPTARG}" ;;
> *) return 1 ;;
> esac
> done
>
> [[ -z "${type}" ]] &&
> {
> echo "Warning: Argument \"type\" is empty; stopping the function"
> return 1
> }
> [[ -z "${MAPQ}" ]] && MAPQ=0
> [[ -z "${file}" ]] &&
> {
> echo "Warning: Argument \"file\" is empty; stopping the function"
> return 1
> }
> [[ -z "${Mito}" ]] && Mito=FALSE
>
> debug=FALSE
> [[ "${debug}" == TRUE ]] &&
> {
> type="all"
> MAPQ=0
> file="${i}"
> Mito=FALSE
>
> echo "${type}"
> echo "${MAPQ}"
> echo "${file}"
> echo "${Mito}"
> }
>
> # All alignments
> [[ "${type}" == "all" ]] &&
> {
> if [[ "${Mito}" == TRUE || "${Mito}" == T ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}"
> )"
> elif [[ "${Mito}" == FALSE ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}" \
> I II III IV V VI VII VIII IX X \
> XI XII XIII XIV XV XVI \
> SP_II_TG SP_I SP_II SP_III SP_MTR
> )"
> fi
>
> echo "${tally}" && return 0
> }
>
>
> # S. cerevisiae alignments only
> [[ "${type}" == "SC" || "${type}" == "sc" || "${type}" == "Sc" ]] &&
> {
> if [[ "${Mito}" == TRUE ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}" \
> I II III IV V VI VII VIII IX X \
> XI XII XIII XIV XV XVI Mito
> )"
> elif [[ "${Mito}" == FALSE ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}" \
> I II III IV V VI VII VIII IX X \
> XI XII XIII XIV XV XVI
> )"
> fi
>
> echo "${tally}" && return 0
> }
>
> # S. pombe alignments only
> [[ "${type}" == "SP" || "${type}" == "sp" || "${type}" == "Sp" ]] &&
> {
> if [[ "${Mito}" == TRUE ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}" \
> SP_II_TG SP_I SP_II SP_III SP_MTR SP_Mito
> )"
> elif [[ "${Mito}" == FALSE ]]; then
> tally="$(
> samtools view -c \
> -F 4 \
> -q "${MAPQ}" \
> "${file}" \
> SP_II_TG SP_I SP_II SP_III SP_MTR
> )"
> fi
>
> echo "${tally}" && return 0
> }
> }
❯ transpose_values() {
> matrix="$(
> awk '
> {
> # Loop through each line and each field (column) in the input
> #+ file, storing the value of each field in the array "a" indexed
> #+ by the column number "i" and the row number "NR"
> for (i = 1; i <= NF; i++) {
> a[i, NR] = $i
> }
> }
> END {
> # Loop through the stored values in the array "a" and print the
> #+ transposed values
> for (i = 1; i <= NF; i++) {
> for (j = 1; j <= NR; j++) {
> printf "%s", a[i, j]
> if (j < NR) {
> printf " "
> }
> }
> print ""
> }
> }
> ' "${1}"
> )"
>
> echo "${matrix}" && return 0
> }
❯ export -f calc_6f
❯ export -f calc_2f
❯ export -f tally_alignments
❯ export -f transpose_valuesPrinted
❯ module purge
❯ ml SAMtools/1.16.1-GCC-11.2.0 Bowtie2/2.4.4-GCC-11.2.0
❯ cd "${HOME}/tsukiyamalab/Kris/2023_rDNA/results" ||
> echo "cd'ing failed; check on this..."
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams"
❯ typeset -a bams=(
> "${p_data}/in_log_WT_Brn1_rep1.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep1.atria.bam"
> "${p_data}/in_log_WT_Brn1_rep2.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep2.atria.bam"
> "${p_data}/in_log_WT_Brn1_rep3.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_rep3.atria.bam"
> "${p_data}/in_log_WT_Brn1_repM.atria.bam"
> "${p_data}/Ch_log_WT_Brn1_repM.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep1.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep1.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep2.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep2.atria.bam"
> "${p_data}/in_Q_WT_Brn1_rep3.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_rep3.atria.bam"
> "${p_data}/in_Q_WT_Brn1_repM.atria.bam"
> "${p_data}/Ch_Q_WT_Brn1_repM.atria.bam"
> )
❯ run_check=TRUE
❯ [[ "${run_check}" == TRUE ]] && \
> for i in "${bams[@]}"; do ls -lhaFG "${i}"; done
-rw-rw---- 1 kalavatt 348M Jul 16 21:21 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 132M Jul 16 15:59 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 279M Jul 16 21:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 585M Jul 16 20:31 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 199M Jul 16 21:23 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 180M Jul 16 20:31 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 781M Jul 16 22:20 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_log_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 863M Jul 16 21:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_log_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 257M Jul 16 22:21 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 172M Jul 16 21:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep1.atria.bam
-rw-rw---- 1 kalavatt 294M Jul 16 22:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 150M Jul 16 21:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep2.atria.bam
-rw-rw---- 1 kalavatt 249M Jul 16 22:22 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 209M Jul 16 21:18 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_rep3.atria.bam
-rw-rw---- 1 kalavatt 756M Jul 16 22:50 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/in_Q_WT_Brn1_repM.atria.bam
-rw-rw---- 1 kalavatt 506M Jul 16 21:20 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Ch_Q_WT_Brn1_repM.atria.bamPrinted
#### in_log_WT_Brn1_rep1.atria.bam ####
in_log_WT_Brn1_rep1
------------------------------------------------------------
"${tallies[${unmapped}]}" 333904
"${tallies[${mapped}]}" 13549404
"${tallies[${total_with_Mito}]}" 13883308
"${tallies[${total_SC_with_Mito}]}" 13258095
"${tallies[${total_SP_with_Mito}]}" 291309
"${tallies[${total_sans_Mito}]}" 12972893
"${tallies[${total_SC_sans_Mito}]}" 12706090
"${tallies[${total_SP_sans_Mito}]}" 266803
"${tallies[${total_SC_Mito}]}" 552005
"${tallies[${total_SP_Mito}]}" 24506
"${tallies[${total_1}]}" 12959145
"${tallies[${total_2}]}" 10473556
"${tallies[${total_3}]}" 10472049
"${tallies[${total_23}]}" 10454533
"${tallies[${total_30}]}" 10413321
"${tallies[${total_40}]}" 10265586
"${tallies[${total_42}]}" 10074757
"${tallies[${SC_0}]}" 12706090
"${tallies[${SC_1}]}" 12692504
"${tallies[${SC_2}]}" 10300915
"${tallies[${SC_3}]}" 10299428
"${tallies[${SC_23}]}" 10282048
"${tallies[${SC_30}]}" 10240927
"${tallies[${SC_40}]}" 10095174
"${tallies[${SC_42}]}" 9905209
"${tallies[${SP_0}]}" 266803
"${tallies[${SP_1}]}" 266641
"${tallies[${SP_2}]}" 172641
"${tallies[${SP_3}]}" 172621
"${tallies[${SP_23}]}" 172485
"${tallies[${SP_30}]}" 172394
"${tallies[${SP_40}]}" 170412
"${tallies[${SP_42}]}" 169548
"${tallies[${CC_SP2SC_0}]}" 0.020998
"${tallies[${CC_SP2SC_1}]}" 0.021008
"${tallies[${CC_SP2SC_2}]}" 0.016760
"${tallies[${CC_SP2SC_3}]}" 0.016760
"${tallies[${CC_SP2SC_23}]}" 0.016775
"${tallies[${CC_SP2SC_30}]}" 0.016834
"${tallies[${CC_SP2SC_40}]}" 0.016881
"${tallies[${CC_SP2SC_42}]}" 0.017117
#### Ch_log_WT_Brn1_rep1.atria.bam ####
Ch_log_WT_Brn1_rep1
------------------------------------------------------------
"${tallies[${unmapped}]}" 499911
"${tallies[${mapped}]}" 5752746
"${tallies[${total_with_Mito}]}" 6252657
"${tallies[${total_SC_with_Mito}]}" 5609097
"${tallies[${total_SP_with_Mito}]}" 143649
"${tallies[${total_sans_Mito}]}" 5740916
"${tallies[${total_SC_sans_Mito}]}" 5597556
"${tallies[${total_SP_sans_Mito}]}" 143360
"${tallies[${total_SC_Mito}]}" 11541
"${tallies[${total_SP_Mito}]}" 289
"${tallies[${total_1}]}" 5722062
"${tallies[${total_2}]}" 3098907
"${tallies[${total_3}]}" 3096507
"${tallies[${total_23}]}" 3085337
"${tallies[${total_30}]}" 3065407
"${tallies[${total_40}]}" 2998196
"${tallies[${total_42}]}" 2934584
"${tallies[${SC_0}]}" 5597556
"${tallies[${SC_1}]}" 5578873
"${tallies[${SC_2}]}" 3059048
"${tallies[${SC_3}]}" 3056672
"${tallies[${SC_23}]}" 3045575
"${tallies[${SC_30}]}" 3025669
"${tallies[${SC_40}]}" 2959163
"${tallies[${SC_42}]}" 2895786
"${tallies[${SP_0}]}" 143360
"${tallies[${SP_1}]}" 143189
"${tallies[${SP_2}]}" 39859
"${tallies[${SP_3}]}" 39835
"${tallies[${SP_23}]}" 39762
"${tallies[${SP_30}]}" 39738
"${tallies[${SP_40}]}" 39033
"${tallies[${SP_42}]}" 38798
"${tallies[${CC_SP2SC_0}]}" 0.025611
"${tallies[${CC_SP2SC_1}]}" 0.025666
"${tallies[${CC_SP2SC_2}]}" 0.013030
"${tallies[${CC_SP2SC_3}]}" 0.013032
"${tallies[${CC_SP2SC_23}]}" 0.013056
"${tallies[${CC_SP2SC_30}]}" 0.013134
"${tallies[${CC_SP2SC_40}]}" 0.013191
"${tallies[${CC_SP2SC_42}]}" 0.013398
#### in_log_WT_Brn1_rep2.atria.bam ####
in_log_WT_Brn1_rep2
------------------------------------------------------------
"${tallies[${unmapped}]}" 236372
"${tallies[${mapped}]}" 10812469
"${tallies[${total_with_Mito}]}" 11048841
"${tallies[${total_SC_with_Mito}]}" 10571481
"${tallies[${total_SP_with_Mito}]}" 240988
"${tallies[${total_sans_Mito}]}" 10384551
"${tallies[${total_SC_sans_Mito}]}" 10162156
"${tallies[${total_SP_sans_Mito}]}" 222395
"${tallies[${total_SC_Mito}]}" 409325
"${tallies[${total_SP_Mito}]}" 18593
"${tallies[${total_1}]}" 10373037
"${tallies[${total_2}]}" 8254098
"${tallies[${total_3}]}" 8252807
"${tallies[${total_23}]}" 8238780
"${tallies[${total_30}]}" 8206403
"${tallies[${total_40}]}" 8090425
"${tallies[${total_42}]}" 7941054
"${tallies[${SC_0}]}" 10162156
"${tallies[${SC_1}]}" 10150752
"${tallies[${SC_2}]}" 8112719
"${tallies[${SC_3}]}" 8111449
"${tallies[${SC_23}]}" 8097546
"${tallies[${SC_30}]}" 8065242
"${tallies[${SC_40}]}" 7950863
"${tallies[${SC_42}]}" 7802230
"${tallies[${SP_0}]}" 222395
"${tallies[${SP_1}]}" 222285
"${tallies[${SP_2}]}" 141379
"${tallies[${SP_3}]}" 141358
"${tallies[${SP_23}]}" 141234
"${tallies[${SP_30}]}" 141161
"${tallies[${SP_40}]}" 139562
"${tallies[${SP_42}]}" 138824
"${tallies[${CC_SP2SC_0}]}" 0.021885
"${tallies[${CC_SP2SC_1}]}" 0.021898
"${tallies[${CC_SP2SC_2}]}" 0.017427
"${tallies[${CC_SP2SC_3}]}" 0.017427
"${tallies[${CC_SP2SC_23}]}" 0.017442
"${tallies[${CC_SP2SC_30}]}" 0.017502
"${tallies[${CC_SP2SC_40}]}" 0.017553
"${tallies[${CC_SP2SC_42}]}" 0.017793
#### Ch_log_WT_Brn1_rep2.atria.bam ####
Ch_log_WT_Brn1_rep2
------------------------------------------------------------
"${tallies[${unmapped}]}" 2734535
"${tallies[${mapped}]}" 27454714
"${tallies[${total_with_Mito}]}" 30189249
"${tallies[${total_SC_with_Mito}]}" 26743282
"${tallies[${total_SP_with_Mito}]}" 711432
"${tallies[${total_sans_Mito}]}" 27353401
"${tallies[${total_SC_sans_Mito}]}" 26644138
"${tallies[${total_SP_sans_Mito}]}" 709263
"${tallies[${total_SC_Mito}]}" 99144
"${tallies[${total_SP_Mito}]}" 2169
"${tallies[${total_1}]}" 27262603
"${tallies[${total_2}]}" 14684393
"${tallies[${total_3}]}" 14673732
"${tallies[${total_23}]}" 14620998
"${tallies[${total_30}]}" 14525548
"${tallies[${total_40}]}" 14211401
"${tallies[${total_42}]}" 13913155
"${tallies[${SC_0}]}" 26644138
"${tallies[${SC_1}]}" 26554208
"${tallies[${SC_2}]}" 14478204
"${tallies[${SC_3}]}" 14467671
"${tallies[${SC_23}]}" 14415347
"${tallies[${SC_30}]}" 14320032
"${tallies[${SC_40}]}" 14009964
"${tallies[${SC_42}]}" 13713002
"${tallies[${SP_0}]}" 709263
"${tallies[${SP_1}]}" 708395
"${tallies[${SP_2}]}" 206189
"${tallies[${SP_3}]}" 206061
"${tallies[${SP_23}]}" 205651
"${tallies[${SP_30}]}" 205516
"${tallies[${SP_40}]}" 201437
"${tallies[${SP_42}]}" 200153
"${tallies[${CC_SP2SC_0}]}" 0.026620
"${tallies[${CC_SP2SC_1}]}" 0.026677
"${tallies[${CC_SP2SC_2}]}" 0.014241
"${tallies[${CC_SP2SC_3}]}" 0.014243
"${tallies[${CC_SP2SC_23}]}" 0.014266
"${tallies[${CC_SP2SC_30}]}" 0.014352
"${tallies[${CC_SP2SC_40}]}" 0.014378
"${tallies[${CC_SP2SC_42}]}" 0.014596
#### in_log_WT_Brn1_rep3.atria.bam ####
in_log_WT_Brn1_rep3
------------------------------------------------------------
"${tallies[${unmapped}]}" 195541
"${tallies[${mapped}]}" 8066952
"${tallies[${total_with_Mito}]}" 8262493
"${tallies[${total_SC_with_Mito}]}" 8027800
"${tallies[${total_SP_with_Mito}]}" 39152
"${tallies[${total_sans_Mito}]}" 7587636
"${tallies[${total_SC_sans_Mito}]}" 7548484
"${tallies[${total_SP_sans_Mito}]}" 39152
"${tallies[${total_SC_Mito}]}" 479316
"${tallies[${total_SP_Mito}]}" 0
"${tallies[${total_1}]}" 7578953
"${tallies[${total_2}]}" 6200891
"${tallies[${total_3}]}" 6199862
"${tallies[${total_23}]}" 6188627
"${tallies[${total_30}]}" 6162439
"${tallies[${total_40}]}" 6074756
"${tallies[${total_42}]}" 5917888
"${tallies[${SC_0}]}" 7548484
"${tallies[${SC_1}]}" 7539870
"${tallies[${SC_2}]}" 6200843
"${tallies[${SC_3}]}" 6199830
"${tallies[${SC_23}]}" 6188614
"${tallies[${SC_30}]}" 6162429
"${tallies[${SC_40}]}" 6074756
"${tallies[${SC_42}]}" 5917888
"${tallies[${SP_0}]}" 39152
"${tallies[${SP_1}]}" 39083
"${tallies[${SP_2}]}" 48
"${tallies[${SP_3}]}" 32
"${tallies[${SP_23}]}" 13
"${tallies[${SP_30}]}" 10
"${tallies[${SP_40}]}" 0
"${tallies[${SP_42}]}" 0
"${tallies[${CC_SP2SC_0}]}" 0.005187
"${tallies[${CC_SP2SC_1}]}" 0.005184
"${tallies[${CC_SP2SC_2}]}" 0.000008
"${tallies[${CC_SP2SC_3}]}" 0.000005
"${tallies[${CC_SP2SC_23}]}" 0.000002
"${tallies[${CC_SP2SC_30}]}" 0.000002
"${tallies[${CC_SP2SC_40}]}" 0.000000
"${tallies[${CC_SP2SC_42}]}" 0.000000
#### Ch_log_WT_Brn1_rep3.atria.bam ####
Ch_log_WT_Brn1_rep3
------------------------------------------------------------
"${tallies[${unmapped}]}" 316828
"${tallies[${mapped}]}" 7851602
"${tallies[${total_with_Mito}]}" 8168430
"${tallies[${total_SC_with_Mito}]}" 7768424
"${tallies[${total_SP_with_Mito}]}" 83178
"${tallies[${total_sans_Mito}]}" 7698275
"${tallies[${total_SC_sans_Mito}]}" 7615097
"${tallies[${total_SP_sans_Mito}]}" 83178
"${tallies[${total_SC_Mito}]}" 153327
"${tallies[${total_SP_Mito}]}" 0
"${tallies[${total_1}]}" 7677910
"${tallies[${total_2}]}" 4984373
"${tallies[${total_3}]}" 4982252
"${tallies[${total_23}]}" 4968750
"${tallies[${total_30}]}" 4941082
"${tallies[${total_40}]}" 4847398
"${tallies[${total_42}]}" 4728066
"${tallies[${SC_0}]}" 7615097
"${tallies[${SC_1}]}" 7594867
"${tallies[${SC_2}]}" 4984274
"${tallies[${SC_3}]}" 4982179
"${tallies[${SC_23}]}" 4968721
"${tallies[${SC_30}]}" 4941058
"${tallies[${SC_40}]}" 4847395
"${tallies[${SC_42}]}" 4728066
"${tallies[${SP_0}]}" 83178
"${tallies[${SP_1}]}" 83043
"${tallies[${SP_2}]}" 99
"${tallies[${SP_3}]}" 73
"${tallies[${SP_23}]}" 29
"${tallies[${SP_30}]}" 24
"${tallies[${SP_40}]}" 3
"${tallies[${SP_42}]}" 0
"${tallies[${CC_SP2SC_0}]}" 0.010923
"${tallies[${CC_SP2SC_1}]}" 0.010934
"${tallies[${CC_SP2SC_2}]}" 0.000020
"${tallies[${CC_SP2SC_3}]}" 0.000015
"${tallies[${CC_SP2SC_23}]}" 0.000006
"${tallies[${CC_SP2SC_30}]}" 0.000005
"${tallies[${CC_SP2SC_40}]}" 0.000001
"${tallies[${CC_SP2SC_42}]}" 0.000000
#### in_log_WT_Brn1_repM.atria.bam ####
in_log_WT_Brn1_repM
------------------------------------------------------------
"${tallies[${unmapped}]}" 765891
"${tallies[${mapped}]}" 32428751
"${tallies[${total_with_Mito}]}" 33194642
"${tallies[${total_SC_with_Mito}]}" 31856761
"${tallies[${total_SP_with_Mito}]}" 571990
"${tallies[${total_sans_Mito}]}" 30945015
"${tallies[${total_SC_sans_Mito}]}" 30416127
"${tallies[${total_SP_sans_Mito}]}" 528888
"${tallies[${total_SC_Mito}]}" 1440634
"${tallies[${total_SP_Mito}]}" 43102
"${tallies[${total_1}]}" 30911132
"${tallies[${total_2}]}" 24928560
"${tallies[${total_3}]}" 24924677
"${tallies[${total_23}]}" 24881929
"${tallies[${total_30}]}" 24782146
"${tallies[${total_40}]}" 24430838
"${tallies[${total_42}]}" 23933786
"${tallies[${SC_0}]}" 30416127
"${tallies[${SC_1}]}" 30382591
"${tallies[${SC_2}]}" 24614485
"${tallies[${SC_3}]}" 24610669
"${tallies[${SC_23}]}" 24568200
"${tallies[${SC_30}]}" 24468582
"${tallies[${SC_40}]}" 24120863
"${tallies[${SC_42}]}" 23625412
"${tallies[${SP_0}]}" 528888
"${tallies[${SP_1}]}" 528541
"${tallies[${SP_2}]}" 314075
"${tallies[${SP_3}]}" 314008
"${tallies[${SP_23}]}" 313729
"${tallies[${SP_30}]}" 313564
"${tallies[${SP_40}]}" 309975
"${tallies[${SP_42}]}" 308374
"${tallies[${CC_SP2SC_0}]}" 0.017388
"${tallies[${CC_SP2SC_1}]}" 0.017396
"${tallies[${CC_SP2SC_2}]}" 0.012760
"${tallies[${CC_SP2SC_3}]}" 0.012759
"${tallies[${CC_SP2SC_23}]}" 0.012770
"${tallies[${CC_SP2SC_30}]}" 0.012815
"${tallies[${CC_SP2SC_40}]}" 0.012851
"${tallies[${CC_SP2SC_42}]}" 0.013053
#### Ch_log_WT_Brn1_repM.atria.bam ####
Ch_log_WT_Brn1_repM
------------------------------------------------------------
"${tallies[${unmapped}]}" 3551257
"${tallies[${mapped}]}" 41059079
"${tallies[${total_with_Mito}]}" 44610336
"${tallies[${total_SC_with_Mito}]}" 40120529
"${tallies[${total_SP_with_Mito}]}" 938550
"${tallies[${total_sans_Mito}]}" 40792626
"${tallies[${total_SC_sans_Mito}]}" 39856529
"${tallies[${total_SP_sans_Mito}]}" 936097
"${tallies[${total_SC_Mito}]}" 264000
"${tallies[${total_SP_Mito}]}" 2453
"${tallies[${total_1}]}" 40662442
"${tallies[${total_2}]}" 22767532
"${tallies[${total_3}]}" 22752335
"${tallies[${total_23}]}" 22674868
"${tallies[${total_30}]}" 22531987
"${tallies[${total_40}]}" 22057002
"${tallies[${total_42}]}" 21575776
"${tallies[${SC_0}]}" 39856529
"${tallies[${SC_1}]}" 39727524
"${tallies[${SC_2}]}" 22521397
"${tallies[${SC_3}]}" 22506372
"${tallies[${SC_23}]}" 22429428
"${tallies[${SC_30}]}" 22286712
"${tallies[${SC_40}]}" 21816532
"${tallies[${SC_42}]}" 21336825
"${tallies[${SP_0}]}" 936097
"${tallies[${SP_1}]}" 934918
"${tallies[${SP_2}]}" 246135
"${tallies[${SP_3}]}" 245963
"${tallies[${SP_23}]}" 245440
"${tallies[${SP_30}]}" 245275
"${tallies[${SP_40}]}" 240470
"${tallies[${SP_42}]}" 238951
"${tallies[${CC_SP2SC_0}]}" 0.023487
"${tallies[${CC_SP2SC_1}]}" 0.023533
"${tallies[${CC_SP2SC_2}]}" 0.010929
"${tallies[${CC_SP2SC_3}]}" 0.010929
"${tallies[${CC_SP2SC_23}]}" 0.010943
"${tallies[${CC_SP2SC_30}]}" 0.011005
"${tallies[${CC_SP2SC_40}]}" 0.011022
"${tallies[${CC_SP2SC_42}]}" 0.011199
#### in_Q_WT_Brn1_rep1.atria.bam ####
in_Q_WT_Brn1_rep1
------------------------------------------------------------
"${tallies[${unmapped}]}" 220686
"${tallies[${mapped}]}" 10099271
"${tallies[${total_with_Mito}]}" 10319957
"${tallies[${total_SC_with_Mito}]}" 9902653
"${tallies[${total_SP_with_Mito}]}" 196618
"${tallies[${total_sans_Mito}]}" 9062225
"${tallies[${total_SC_sans_Mito}]}" 8879315
"${tallies[${total_SP_sans_Mito}]}" 182910
"${tallies[${total_SC_Mito}]}" 1023338
"${tallies[${total_SP_Mito}]}" 13708
"${tallies[${total_1}]}" 9051915
"${tallies[${total_2}]}" 6908730
"${tallies[${total_3}]}" 6907543
"${tallies[${total_23}]}" 6895343
"${tallies[${total_30}]}" 6868153
"${tallies[${total_40}]}" 6768007
"${tallies[${total_42}]}" 6644434
"${tallies[${SC_0}]}" 8879315
"${tallies[${SC_1}]}" 8869108
"${tallies[${SC_2}]}" 6807940
"${tallies[${SC_3}]}" 6806770
"${tallies[${SC_23}]}" 6794672
"${tallies[${SC_30}]}" 6767541
"${tallies[${SC_40}]}" 6668609
"${tallies[${SC_42}]}" 6545581
"${tallies[${SP_0}]}" 182910
"${tallies[${SP_1}]}" 182807
"${tallies[${SP_2}]}" 100790
"${tallies[${SP_3}]}" 100773
"${tallies[${SP_23}]}" 100671
"${tallies[${SP_30}]}" 100612
"${tallies[${SP_40}]}" 99398
"${tallies[${SP_42}]}" 98853
"${tallies[${CC_SP2SC_0}]}" 0.020600
"${tallies[${CC_SP2SC_1}]}" 0.020612
"${tallies[${CC_SP2SC_2}]}" 0.014805
"${tallies[${CC_SP2SC_3}]}" 0.014805
"${tallies[${CC_SP2SC_23}]}" 0.014816
"${tallies[${CC_SP2SC_30}]}" 0.014867
"${tallies[${CC_SP2SC_40}]}" 0.014905
"${tallies[${CC_SP2SC_42}]}" 0.015102
#### Ch_Q_WT_Brn1_rep1.atria.bam ####
Ch_Q_WT_Brn1_rep1
------------------------------------------------------------
"${tallies[${unmapped}]}" 1739181
"${tallies[${mapped}]}" 5492116
"${tallies[${total_with_Mito}]}" 7231297
"${tallies[${total_SC_with_Mito}]}" 5253236
"${tallies[${total_SP_with_Mito}]}" 238880
"${tallies[${total_sans_Mito}]}" 5369372
"${tallies[${total_SC_sans_Mito}]}" 5137368
"${tallies[${total_SP_sans_Mito}]}" 232004
"${tallies[${total_SC_Mito}]}" 115868
"${tallies[${total_SP_Mito}]}" 6876
"${tallies[${total_1}]}" 5359911
"${tallies[${total_2}]}" 3745001
"${tallies[${total_3}]}" 3743611
"${tallies[${total_23}]}" 3734792
"${tallies[${total_30}]}" 3717664
"${tallies[${total_40}]}" 3658456
"${tallies[${total_42}]}" 3579279
"${tallies[${SC_0}]}" 5137368
"${tallies[${SC_1}]}" 5128233
"${tallies[${SC_2}]}" 3597499
"${tallies[${SC_3}]}" 3596131
"${tallies[${SC_23}]}" 3587470
"${tallies[${SC_30}]}" 3570424
"${tallies[${SC_40}]}" 3513649
"${tallies[${SC_42}]}" 3435400
"${tallies[${SP_0}]}" 232004
"${tallies[${SP_1}]}" 231678
"${tallies[${SP_2}]}" 147502
"${tallies[${SP_3}]}" 147480
"${tallies[${SP_23}]}" 147322
"${tallies[${SP_30}]}" 147240
"${tallies[${SP_40}]}" 144807
"${tallies[${SP_42}]}" 143879
"${tallies[${CC_SP2SC_0}]}" 0.045160
"${tallies[${CC_SP2SC_1}]}" 0.045177
"${tallies[${CC_SP2SC_2}]}" 0.041001
"${tallies[${CC_SP2SC_3}]}" 0.041011
"${tallies[${CC_SP2SC_23}]}" 0.041066
"${tallies[${CC_SP2SC_30}]}" 0.041239
"${tallies[${CC_SP2SC_40}]}" 0.041213
"${tallies[${CC_SP2SC_42}]}" 0.041881
#### in_Q_WT_Brn1_rep2.atria.bam ####
in_Q_WT_Brn1_rep2
------------------------------------------------------------
"${tallies[${unmapped}]}" 217378
"${tallies[${mapped}]}" 11713482
"${tallies[${total_with_Mito}]}" 11930860
"${tallies[${total_SC_with_Mito}]}" 11444841
"${tallies[${total_SP_with_Mito}]}" 268641
"${tallies[${total_sans_Mito}]}" 10908066
"${tallies[${total_SC_sans_Mito}]}" 10657329
"${tallies[${total_SP_sans_Mito}]}" 250737
"${tallies[${total_SC_Mito}]}" 787512
"${tallies[${total_SP_Mito}]}" 17904
"${tallies[${total_1}]}" 10895153
"${tallies[${total_2}]}" 7956792
"${tallies[${total_3}]}" 7955394
"${tallies[${total_23}]}" 7940826
"${tallies[${total_30}]}" 7908496
"${tallies[${total_40}]}" 7792753
"${tallies[${total_42}]}" 7649588
"${tallies[${SC_0}]}" 10657329
"${tallies[${SC_1}]}" 10644568
"${tallies[${SC_2}]}" 7822379
"${tallies[${SC_3}]}" 7821009
"${tallies[${SC_23}]}" 7806582
"${tallies[${SC_30}]}" 7774331
"${tallies[${SC_40}]}" 7660119
"${tallies[${SC_42}]}" 7517642
"${tallies[${SP_0}]}" 250737
"${tallies[${SP_1}]}" 250585
"${tallies[${SP_2}]}" 134413
"${tallies[${SP_3}]}" 134385
"${tallies[${SP_23}]}" 134244
"${tallies[${SP_30}]}" 134165
"${tallies[${SP_40}]}" 132634
"${tallies[${SP_42}]}" 131946
"${tallies[${CC_SP2SC_0}]}" 0.023527
"${tallies[${CC_SP2SC_1}]}" 0.023541
"${tallies[${CC_SP2SC_2}]}" 0.017183
"${tallies[${CC_SP2SC_3}]}" 0.017183
"${tallies[${CC_SP2SC_23}]}" 0.017196
"${tallies[${CC_SP2SC_30}]}" 0.017257
"${tallies[${CC_SP2SC_40}]}" 0.017315
"${tallies[${CC_SP2SC_42}]}" 0.017552
#### Ch_Q_WT_Brn1_rep2.atria.bam ####
Ch_Q_WT_Brn1_rep2
------------------------------------------------------------
"${tallies[${unmapped}]}" 1066876
"${tallies[${mapped}]}" 5421690
"${tallies[${total_with_Mito}]}" 6488566
"${tallies[${total_SC_with_Mito}]}" 5202988
"${tallies[${total_SP_with_Mito}]}" 218702
"${tallies[${total_sans_Mito}]}" 5350248
"${tallies[${total_SC_sans_Mito}]}" 5137697
"${tallies[${total_SP_sans_Mito}]}" 212551
"${tallies[${total_SC_Mito}]}" 65291
"${tallies[${total_SP_Mito}]}" 6151
"${tallies[${total_1}]}" 5341736
"${tallies[${total_2}]}" 3442540
"${tallies[${total_3}]}" 3441459
"${tallies[${total_23}]}" 3433073
"${tallies[${total_30}]}" 3415828
"${tallies[${total_40}]}" 3360434
"${tallies[${total_42}]}" 3286560
"${tallies[${SC_0}]}" 5137697
"${tallies[${SC_1}]}" 5129454
"${tallies[${SC_2}]}" 3321989
"${tallies[${SC_3}]}" 3320927
"${tallies[${SC_23}]}" 3312680
"${tallies[${SC_30}]}" 3295510
"${tallies[${SC_40}]}" 3242161
"${tallies[${SC_42}]}" 3169083
"${tallies[${SP_0}]}" 212551
"${tallies[${SP_1}]}" 212282
"${tallies[${SP_2}]}" 120551
"${tallies[${SP_3}]}" 120532
"${tallies[${SP_23}]}" 120393
"${tallies[${SP_30}]}" 120318
"${tallies[${SP_40}]}" 118273
"${tallies[${SP_42}]}" 117477
"${tallies[${CC_SP2SC_0}]}" 0.041371
"${tallies[${CC_SP2SC_1}]}" 0.041385
"${tallies[${CC_SP2SC_2}]}" 0.036289
"${tallies[${CC_SP2SC_3}]}" 0.036295
"${tallies[${CC_SP2SC_23}]}" 0.036343
"${tallies[${CC_SP2SC_30}]}" 0.036510
"${tallies[${CC_SP2SC_40}]}" 0.036480
"${tallies[${CC_SP2SC_42}]}" 0.037070
#### in_Q_WT_Brn1_rep3.atria.bam ####
in_Q_WT_Brn1_rep3
------------------------------------------------------------
"${tallies[${unmapped}]}" 265277
"${tallies[${mapped}]}" 10184624
"${tallies[${total_with_Mito}]}" 10449901
"${tallies[${total_SC_with_Mito}]}" 10143319
"${tallies[${total_SP_with_Mito}]}" 41305
"${tallies[${total_sans_Mito}]}" 9490476
"${tallies[${total_SC_sans_Mito}]}" 9449171
"${tallies[${total_SP_sans_Mito}]}" 41305
"${tallies[${total_SC_Mito}]}" 694148
"${tallies[${total_SP_Mito}]}" 0
"${tallies[${total_1}]}" 9477888
"${tallies[${total_2}]}" 7918342
"${tallies[${total_3}]}" 7916426
"${tallies[${total_23}]}" 7901664
"${tallies[${total_30}]}" 7868730
"${tallies[${total_40}]}" 7755327
"${tallies[${total_42}]}" 7581526
"${tallies[${SC_0}]}" 9449171
"${tallies[${SC_1}]}" 9436650
"${tallies[${SC_2}]}" 7918277
"${tallies[${SC_3}]}" 7916378
"${tallies[${SC_23}]}" 7901651
"${tallies[${SC_30}]}" 7868721
"${tallies[${SC_40}]}" 7755325
"${tallies[${SC_42}]}" 7581526
"${tallies[${SP_0}]}" 41305
"${tallies[${SP_1}]}" 41238
"${tallies[${SP_2}]}" 65
"${tallies[${SP_3}]}" 48
"${tallies[${SP_23}]}" 13
"${tallies[${SP_30}]}" 9
"${tallies[${SP_40}]}" 2
"${tallies[${SP_42}]}" 0
"${tallies[${CC_SP2SC_0}]}" 0.004371
"${tallies[${CC_SP2SC_1}]}" 0.004370
"${tallies[${CC_SP2SC_2}]}" 0.000008
"${tallies[${CC_SP2SC_3}]}" 0.000006
"${tallies[${CC_SP2SC_23}]}" 0.000002
"${tallies[${CC_SP2SC_30}]}" 0.000001
"${tallies[${CC_SP2SC_40}]}" 0.000000
"${tallies[${CC_SP2SC_42}]}" 0.000000
#### Ch_Q_WT_Brn1_rep3.atria.bam ####
Ch_Q_WT_Brn1_rep3
------------------------------------------------------------
"${tallies[${unmapped}]}" 612389
"${tallies[${mapped}]}" 8254445
"${tallies[${total_with_Mito}]}" 8866834
"${tallies[${total_SC_with_Mito}]}" 8178828
"${tallies[${total_SP_with_Mito}]}" 75617
"${tallies[${total_sans_Mito}]}" 8110801
"${tallies[${total_SC_sans_Mito}]}" 8035185
"${tallies[${total_SP_sans_Mito}]}" 75616
"${tallies[${total_SC_Mito}]}" 143643
"${tallies[${total_SP_Mito}]}" 1
"${tallies[${total_1}]}" 8088510
"${tallies[${total_2}]}" 5404473
"${tallies[${total_3}]}" 5400771
"${tallies[${total_23}]}" 5384058
"${tallies[${total_30}]}" 5354027
"${tallies[${total_40}]}" 5256137
"${tallies[${total_42}]}" 5132737
"${tallies[${SC_0}]}" 8035185
"${tallies[${SC_1}]}" 8013026
"${tallies[${SC_2}]}" 5404377
"${tallies[${SC_3}]}" 5400693
"${tallies[${SC_23}]}" 5384039
"${tallies[${SC_30}]}" 5354012
"${tallies[${SC_40}]}" 5256132
"${tallies[${SC_42}]}" 5132735
"${tallies[${SP_0}]}" 75616
"${tallies[${SP_1}]}" 75484
"${tallies[${SP_2}]}" 96
"${tallies[${SP_3}]}" 78
"${tallies[${SP_23}]}" 19
"${tallies[${SP_30}]}" 15
"${tallies[${SP_40}]}" 5
"${tallies[${SP_42}]}" 2
"${tallies[${CC_SP2SC_0}]}" 0.009411
"${tallies[${CC_SP2SC_1}]}" 0.009420
"${tallies[${CC_SP2SC_2}]}" 0.000018
"${tallies[${CC_SP2SC_3}]}" 0.000014
"${tallies[${CC_SP2SC_23}]}" 0.000004
"${tallies[${CC_SP2SC_30}]}" 0.000003
"${tallies[${CC_SP2SC_40}]}" 0.000001
"${tallies[${CC_SP2SC_42}]}" 0.000000
#### in_Q_WT_Brn1_repM.atria.bam ####
in_Q_WT_Brn1_repM
------------------------------------------------------------
"${tallies[${unmapped}]}" 703297
"${tallies[${mapped}]}" 31997421
"${tallies[${total_with_Mito}]}" 32700718
"${tallies[${total_SC_with_Mito}]}" 31490835
"${tallies[${total_SP_with_Mito}]}" 506586
"${tallies[${total_sans_Mito}]}" 29460746
"${tallies[${total_SC_sans_Mito}]}" 28985770
"${tallies[${total_SP_sans_Mito}]}" 474976
"${tallies[${total_SC_Mito}]}" 2505065
"${tallies[${total_SP_Mito}]}" 31610
"${tallies[${total_1}]}" 29424922
"${tallies[${total_2}]}" 22783840
"${tallies[${total_3}]}" 22779363
"${tallies[${total_23}]}" 22737818
"${tallies[${total_30}]}" 22645393
"${tallies[${total_40}]}" 22316141
"${tallies[${total_42}]}" 21875592
"${tallies[${SC_0}]}" 28985770
"${tallies[${SC_1}]}" 28950275
"${tallies[${SC_2}]}" 22548588
"${tallies[${SC_3}]}" 22544159
"${tallies[${SC_23}]}" 22502886
"${tallies[${SC_30}]}" 22410603
"${tallies[${SC_40}]}" 22084100
"${tallies[${SC_42}]}" 21644790
"${tallies[${SP_0}]}" 474976
"${tallies[${SP_1}]}" 474647
"${tallies[${SP_2}]}" 235252
"${tallies[${SP_3}]}" 235204
"${tallies[${SP_23}]}" 234932
"${tallies[${SP_30}]}" 234790
"${tallies[${SP_40}]}" 232041
"${tallies[${SP_42}]}" 230802
"${tallies[${CC_SP2SC_0}]}" 0.016387
"${tallies[${CC_SP2SC_1}]}" 0.016395
"${tallies[${CC_SP2SC_2}]}" 0.010433
"${tallies[${CC_SP2SC_3}]}" 0.010433
"${tallies[${CC_SP2SC_23}]}" 0.010440
"${tallies[${CC_SP2SC_30}]}" 0.010477
"${tallies[${CC_SP2SC_40}]}" 0.010507
"${tallies[${CC_SP2SC_42}]}" 0.010663
#### Ch_Q_WT_Brn1_repM.atria.bam ####
Ch_Q_WT_Brn1_repM
------------------------------------------------------------
"${tallies[${unmapped}]}" 3418392
"${tallies[${mapped}]}" 19168305
"${tallies[${total_with_Mito}]}" 22586697
"${tallies[${total_SC_with_Mito}]}" 18636191
"${tallies[${total_SP_with_Mito}]}" 532114
"${tallies[${total_sans_Mito}]}" 18830521
"${tallies[${total_SC_sans_Mito}]}" 18311441
"${tallies[${total_SP_sans_Mito}]}" 519080
"${tallies[${total_SC_Mito}]}" 324750
"${tallies[${total_SP_Mito}]}" 13034
"${tallies[${total_1}]}" 18790189
"${tallies[${total_2}]}" 12591991
"${tallies[${total_3}]}" 12585830
"${tallies[${total_23}]}" 12551898
"${tallies[${total_30}]}" 12487541
"${tallies[${total_40}]}" 12275084
"${tallies[${total_42}]}" 11998618
"${tallies[${SC_0}]}" 18311441
"${tallies[${SC_1}]}" 18271807
"${tallies[${SC_2}]}" 12323823
"${tallies[${SC_3}]}" 12317741
"${tallies[${SC_23}]}" 12284157
"${tallies[${SC_30}]}" 12219965
"${tallies[${SC_40}]}" 12011998
"${tallies[${SC_42}]}" 11737260
"${tallies[${SP_0}]}" 519080
"${tallies[${SP_1}]}" 518382
"${tallies[${SP_2}]}" 268168
"${tallies[${SP_3}]}" 268089
"${tallies[${SP_23}]}" 267741
"${tallies[${SP_30}]}" 267576
"${tallies[${SP_40}]}" 263086
"${tallies[${SP_42}]}" 261358
"${tallies[${CC_SP2SC_0}]}" 0.028347
"${tallies[${CC_SP2SC_1}]}" 0.028371
"${tallies[${CC_SP2SC_2}]}" 0.021760
"${tallies[${CC_SP2SC_3}]}" 0.021764
"${tallies[${CC_SP2SC_23}]}" 0.021796
"${tallies[${CC_SP2SC_30}]}" 0.021897
"${tallies[${CC_SP2SC_40}]}" 0.021902
"${tallies[${CC_SP2SC_42}]}" 0.022267
❯ cat "${a_tallies}"
sample unmapped mapped total_with_Mito total_SC_with_Mito total_SP_with_Mito total_sans_Mito total_SC_sans_Mito total_SP_sans_Mito total_SC_Mito total_SP_Mito total_1 total_2 total_3 total_23 total_30 total_40 total_42 SC_0 SC_1 SC_2 SC_3 SC_23 SC_30 SC_40 SC_42 SP_0 SP_1 SP_2 SP_3 SP_23 SP_30 SP_40 SP_42 CC_SP2SC_0 CC_SP2SC_1 CC_SP2SC_2 CC_SP2SC_3 CC_SP2SC_23 CC_SP2SC_30 CC_SP2SC_40 CC_SP2SC_42
in_log_WT_Brn1_rep1 333904 13549404 13883308 13258095 291309 12972893 12706090 266803 552005 24506 12959145 10473556 10472049 10454533 10413321 10265586 10074757 12706090 12692504 10300915 10299428 10282048 10240927 10095174 9905209 266803 266641 172641 172621 172485 172394 170412 169548 0.020998 0.021008 0.016760 0.016760 0.016775 0.016834 0.016881 0.017117
Ch_log_WT_Brn1_rep1 499911 5752746 6252657 5609097 143649 5740916 5597556 143360 11541 289 5722062 3098907 3096507 3085337 3065407 2998196 2934584 5597556 5578873 3059048 3056672 3045575 3025669 2959163 2895786 143360 143189 39859 39835 39762 39738 39033 38798 0.025611 0.025666 0.013030 0.013032 0.013056 0.013134 0.013191 0.013398
...
❯ calculate_run_time "${start}" "${end}" \
> "Generate tab-separated table of alignment tallies/calculations."
Generate tab-separated table of alignment tallies/calculations.
Run time: 0h:38m:39sEmail from Christine
Title: ChIP-seq analyses: Friendly reminder to check if, when using deepTools, you input the scaling factors as reciprocals
From: Cucinotta, Christine E
To: Alavattam, Kris
Time: Tue 7/18/2023 1:38 PM
Hi Kris,
I take the Pombe:Sc ratio of all the samples. Then take the ratio of the sample we want to normalize to (e.g., WT or a time zero) and divide by the test sample.
I have trouble writing it out so here’s an example:
Q Pombe:Sc = 0.35 (control)
5m Pombe:Sc = 0.26 (test)
Scaling factor for Q = 0.35/0.35 = 1 (use this for the scaling factor in deeptools) (control/control)
Scaling factor for 5m = 0.35/0.26 = 1.35 (use this number for the scaling factor in deeptools) (control/test)
I hope this makes sense. Please let me know if not – happy to chat!
Thanks!
-Chrsitine
Notes on using Excel to calculate scaling factors
Calculate the scaling factor by hand using the table of tallies/calculations
- Calculate the quotient of a given sample's input SP-to-SC ratio and its ChIP SP-to-SC ratio—this is the scaling factor
- For example, for sample
Brn1_Q_rep1, divide theinputSP-to-SCvalue by theChIPSP-to-SCvalue: 0.019802 ÷ 0.045415 = 0.436023 - Do this for all samples (e.g., sample-and-replicate-wise pairs of input and ChIP
bams)