LASER

Long-reads-based Alternative Splicing Estimation and Recognition

LASER determines the regulatory connections between exons, 5' ends, and 3' ends by analyzing every read as a complete transcript and using multinomial testing to evaluate the frequency of co-occurrence among these features.

Installation

install.packages("devtools")
devtools::install_github("hilgers-lab/LASER", build = TRUE, build_vignettes = FALSE)

Input files

• Genome Alignment bam files minimap2 using parameters minimap2 -ax splice -u f annotation/genome.fa long_read.fastq.gz | samtools sort -@ 4 -o output.bam - samtools index output.bam
• Reference annotation in gtf format. Example file here
• Short read sequencing SJ.out files STAR. Example file in here. We recommend to pull SJ.out into a single SJ.out from many experiments and filter by min counts.

Usage

A step by step guide for data processing and identification of exon-couplings can be found here.

library(LASER)
vignette("LASER")

Release

Initial Release 0.1.0

Release date: 12th May 2023 This release corresponds to the LASER version used by Alfonso-Gonzalez et al. 2023

Contact

Developer Carlos Alfonso-Gonzalez. For questions or feedback you can contact:

[email protected]