rmats2sashimiplot

Introduction

rmats2sashimiplot produces a sashimiplot visualization of rMATS output. rmats2sashimiplot can also produce plots using an annotation file and genomic coordinates. The plotting backend is MISO.

Detailed usage can be found here: https://github.com/Xinglab/rmats2sashimiplot

Versions

• 2.0.4

Commands

• rmats2sashimiplot

Module

You can load the modules by:

module load biocontainers
module load rmats2sashimiplot

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 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=rmats2sashimiplot
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers rmats2sashimiplot

rmats2sashimiplot --s1 sample_1_replicate_1.sam,sample_1_replicate_2.sam,sample_1_replicate_3.sam \
                  --s2 sample_2_replicate_1.sam,sample_2_replicate_2.sam,sample_2_replicate_3.sam \
                  -t SE -e SE.MATS.JC.txt --l1 SampleOne --l2 SampleTwo --exon_s 1 --intron_s 5 \
                  -o test_events_output