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example.ini
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example.ini
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[global]
WORKING_DIR = /home/user/rG4-seq/rG4-seeker_output/
SAMPLE_NAME = example
THREADS = 8
NO_OF_ANNOTATIONS = 1
NO_OF_REPLICATES = 4
HAVE_KPDS_CONDITION = True
ALIGNER = STAR
READS_TYPE = SE
[genome]
GENOME_FASTA = /home/user/references/gencode_human/GRCh38.primary_assembly.genome.fa
GENOME_FASTA_FAI = /home/user/references/gencode_human/GRCh38.primary_assembly.genome.fa.fai
[annotation_1]
ANNOTATION_NAME = 'GENCODE_V29'
ANNOTATION_GFF = /home/user/references/gencode_human/gencode.v29.primary_assembly.annotation.gff3.gz
[replicate_1]
LI_BAM_FILE = /home/user/rG4-seq/Li-rep1.Aligned.sortedByCoord.out.bam
K_BAM_FILE = /home/user/rG4-seq/K-rep1.Aligned.sortedByCoord.out.bam
KPDS_BAM_FILE = /home/user/rG4-seq/KPDS-rep1.Aligned.sortedByCoord.out.bam
[replicate_2]
LI_BAM_FILE = /home/user/rG4-seq/Li-rep2.Aligned.sortedByCoord.out.bam
K_BAM_FILE = /home/user/rG4-seq/K-rep2.Aligned.sortedByCoord.out.bam
KPDS_BAM_FILE = /home/user/rG4-seq/KPDS-rep2.Aligned.sortedByCoord.out.bam
[replicate_3]
LI_BAM_FILE = /home/user/rG4-seq/Li-rep3.Aligned.sortedByCoord.out.bam
K_BAM_FILE = /home/user/rG4-seq/K-rep3.Aligned.sortedByCoord.out.bam
KPDS_BAM_FILE = /home/user/rG4-seq/KPDS-rep3.Aligned.sortedByCoord.out.bam
[replicate_4]
LI_BAM_FILE = /home/user/rG4-seq/Li-rep4.Aligned.sortedByCoord.out.bam
K_BAM_FILE = /home/user/rG4-seq/K-rep4.Aligned.sortedByCoord.out.bam
KPDS_BAM_FILE = /home/user/rG4-seq/KPDS-rep4.Aligned.sortedByCoord.out.bam