Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

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. The replicate MATS (rMATS) is designed for detection of differential alternative splicing from replicate RNA-Seq data.

References:

• Shen S., Park JW., Lu ZX., Lin L., Henry MD., Wu YN., Zhou Q., Xing Y. rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data. PNAS, 111(51):E5593-601. doi: 10.1073/pnas.1419161111

• rMATS home page
• rMATS-long home page
• rMATS Github page

• Module Name: rmats (see the modules page for more information)
• Multithreaded app (set --nthread $SLURM_CPUS_PER_TASK)
• Example files in /usr/local/apps/rmats/TEST_DATA
• Reference data in /fdb/STAR_indices
• Unusual environment variables set
  • RMATS_HOME  installation directory
  • RMATS_BIN  executable directory
  • RMATS_SRC  source code directory
  • RMATS_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive -c 16 --mem 45g --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ mkdir -p /data/$USER/rmats && cd /data/$USER/rmats

Here is how one can use the most recent rMATS version 4.1.2:

[user@cn3144 ~]$ module load rmats/4.1.2
[+] Loading singularity  3.8.5-1  on cn3144
[+] Loading rMATS  4.1.2
[user@cn3144 ~]$  cp -r $RMATS_DATA/* . 

[user@cn3144 ~]$  rmats.py --s1 $PWD/s1.txt --s2 $PWD/s2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_indices/2.7.8a/GENCODE/Gencode_human/release_27/genes-100 --od out_test -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 50 --tophatAnchor 8 --cstat 0.0001 --tstat 6 --tmp /lscratch/${SLURM_JOB_ID} 
...

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. submit.sh). For example:

#!/bin/bash
set -e
module load rmats
export TMPDIR=/lscratch/$SLURM_JOBID
rmats.py  --s1 $PWD/s1.txt --s2 $PWD/s2.txt --gtf $PWD/gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_indices/2.7.8a/GENCODE/Gencode_human/release_27/genes-100 --od out_test -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 50 --tophatAnchor 8 --cstat 0.0001 --tstat 6 --tmp /lscratch/${SLURM_JOB_ID}

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=30g --gres=lscratch:20 submit.sh

Create a swarmfile (e.g. rmats.swarm). For example:

rmats.py  --s1 $PWD/s1.txt --s2 $PWD/s2.txt --gtf $PWDgtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_indices/2.7.8a/GENCODE/Gencode_human/release_27/genes-100 --od out_test1 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 50  --tophatAnchor 8 --cstat 0.0001 --tstat 6 --tmp /lscratch/${SLURM_JOB_ID}
rmats.py  --s1 $PWD s3.txt --s2 $PWD s4.txt --gtf $PWDgtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_indices/2.7.8a/GENCODE/Gencode_human/release_27/genes-100 --od out_test2 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 50  --tophatAnchor 8 --cstat 0.0001 --tstat 6 --tmp /lscratch/${SLURM_JOB_ID}
rmats.py  --s1 $PWD s5.txt --s2 $PWD s6.txt --gtf $PWDgtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_indices/2.7.8a/GENCODE/Gencode_human/release_27/genes-100 --od out_test3 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 50  --tophatAnchor 8 --cstat 0.0001 --tstat 6 --tmp /lscratch/${SLURM_JOB_ID}

Submit this job using the swarm command.

swarm -f rmats.swarm [-g 30] [-t 16] --module rmats

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module TEMPLATE	Loads the TEMPLATE module for each subjob in the swarm