rMATS

Introduction

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.

Detailed usage can be found here: http://rnaseq-mats.sourceforge.net

Versions

4.1.1

Commands

rmats.py

Module

You can load the modules by:

module load biocontainers
module load rmats

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run rmats on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=rmats
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers rmats

rmats.py --b1 SR_b1.txt --b2 SR_b2.txt --gtf Homo_sapiens.GRCh38.105.gtf --od rmats_out_homo --tmp rmats_tmp  -t paired --nthread 10 --readLength 150