This is an old revision of the document!
description
Multivariate Analysis of Transcript Splicing (MATS). MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. Software page : http://rnaseq-mats.sourceforge.net/ .
software version
Below release of rMATS 4.0.21) ( 04/25/2018 ) is described and used.
prepare software
Login to anthill23 and download rMATS along with some test dataset, and gft files:
@anthill23:~$
mkdir -p ~/anthill23_rmats/{testData,gtf}
cd ~/anthill23_rmats
wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.4.0.2.tgz
tar xzf rMATS.4.0.2.tgz
cd ~/anthill23_rmats/testData
wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/testData.tgz
tar xzf testData.tgz
cd ~/anthill23_rmats/gtf
wget ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
gunzip Homo_sapiens.GRCh37.87.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz
gunzip Homo_sapiens.GRCh38.91.gtf.gz
prepare gsl lib
rMATS uses gsl library that need to be prepared separately2). This library have to be compiled on computing node, so it is done in interactive mode ( SLURM, batch and interactive mode) :
@anthill23:~$
srun -N1 -n4 --pty bash -l
cd ~/anthill23_rmats/
wget http://gnu.mirror.vexxhost.com/gsl/gsl-2.4.tar.gz
tar xzf gsl-2.4.tar.gz
cd gsl-2.4
./configure --prefix="/home/users/${USER}/anthill23_rmats/gsl-2.4"
make -j ${SLURM_NTASKS}
make install
cd ~/anthill23_rmats/gsl-2.4/lib
ln -s libgsl.so libgsl.so.0
sbatch example
…
...
performance tests
…
...
1)
rMATS is available in two 'versions'. Version
rMATS-turbo-xxx-UCS4 is one to be used, more http://rnaseq-mats.sourceforge.net/user_guide.htm in section 'Which version to use'2)
takes about five minutes