Biowulf High Performance Computing at the NIH
rMATS on Biowulf

Description: 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.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive -c 16 --mem 45g
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 ~]$ module load rmats

[user@cn3144 ~]$ cd /data/teacher/rmats

[user@cn3144 ~]$ cp -r /usr/local/apps/rmats/testData/* .

[user@cn3144 ~]$ rmats --s1 s1.txt --s2 s2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_current/GENCODE/Gencode_human/release_27/genes-100 --od out_test -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 101 --tophatAnchor 8 --cstat 0.0001 --tstat 6

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

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load rmats
rmats --s1 s1.txt --s2 s2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_current/GENCODE/Gencode_human/release_27/genes-100 --od out_test -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 101 --tophatAnchor 8 --cstat 0.0001 --tstat 6

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=16] [--mem=30g] submit.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

rmats --s1 s1.txt --s2 s2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_current/GENCODE/Gencode_human/release_27/genes-100 --od out_test1 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 101 --tophatAnchor 8 --cstat
rmats --s1 s3.txt --s2 s4.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_current/GENCODE/Gencode_human/release_27/genes-100 --od out_test2 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 101 --tophatAnchor 8 --cstat
rmats --s1 s5.txt --s2 s6.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi /fdb/STAR_current/GENCODE/Gencode_human/release_27/genes-100 --od out_test3 -t paired --nthread $SLURM_CPUS_PER_TASK --readLength 101 --tophatAnchor 8 --cstat

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