rMATS (Docker)

Docker to run rMATS for splicing quantification and analysis

Available software

• rMATS 3.2.5 (run using python ${rmats}/RNASeq-MATS.py)
• samtools 1.5
• STAR 2.5.3a
• python 2.7

Maintainer

Nuno Agostinho - Nuno Morais Lab, iMM (2017)

Building

docker build . -t rdeboo/rmats:4.0.2-3

Testing

#download test data
mkdir data
wget -qO- https://datapacket.dl.sourceforge.net/project/rnaseq-mats/MATS/gtf.tgz | tar xvz -C data/
wget -qO- https://netcologne.dl.sourceforge.net/project/rnaseq-mats/MATS/testData.tgz | tar xvz -C data/

# run container
docker run -ti -v $(pwd)data:/data rdeboo/rmats:4.0.2-3 bash

# run these commands inside container
cd /data/testData

python /root/software/rmats/rMATS-turbo-Linux-UCS4/rmats.py \
--b1 /data/testData/b1.txt --b2 /data/testData/b2.txt \
--gtf /data/gtf/Homo_sapiens.Ensembl.GRCh37.75.gtf \
--od /data/output -t paired --readLength 101 --cstat 0.0001 --libType fr-unstranded

Note that the output is written in /data which is a directory on the host VM. Therefore the output is persisted after the docker container is exited.