Docker to run rMATS for splicing quantification and analysis
- rMATS 3.2.5 (run using
python ${rmats}/RNASeq-MATS.py) - samtools 1.5
- STAR 2.5.3a
- python 2.7
Nuno Agostinho - Nuno Morais Lab, iMM (2017)
docker build . -t rdeboo/rmats:4.0.2-3
#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.