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==== 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 4.0.2((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')) ( 04/25/2018 ) is described and used.

==== prepare software ====
Login to anthill23 and download rMATS along with some test datasets, and gft files((downloading this files will take about 3 minutes)):

  @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

==== prepare gsl lib ====
rMATS uses gsl library that need to be prepared separately((takes about five minutes)). This library have to be compiled on computing node, so it is done in interactive mode ([[howtouseslurm_000|SLURM, batch and interactive mode]]) :

  @anthill23:~$
  
  srun -J gsl_compile -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
  
  exit

==== simple test ====
If above steps ( prepare software, and prepare gsl lib ) finish successfully this simple test should finish with success. Do this test in  interactive mode ([[howtouseslurm_000|SLURM, batch and interactive mode]]) :

  @anthill23:~$
  
  srun -J rMATS_test --pty bash -l
  
  cd /home/users/${USER}/anthill23_rmats
  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib
  python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 testData/b1.txt --b2 testData/b2.txt --gtf gtf/Homo_sapiens.GRCh37.87.gtf --od bam_test -t paired --readLength 50 --cstat 0.0001 --libType fr-unstranded
  
  ...
  #read output and exit interactive mode when finished
  exit

==== sbatch example ====
Bellow example was taken form [[http://rnaseq-mats.sourceforge.net/user_guide.htm|rMATS User Guide]]. This description assumes that above steps ( prepare software, and prepare gsl lib ) were done beforehand if not, remember to modify them accordingly. 

File ''rmats_test.batch'' . 

<code>
#!/bin/bash -l
#SBATCH --partition=test
#SBATCH --ntasks=4
#SBATCH --mem 4G
#SBATCH --job-name rMATS_test

cd /home/users/${USER}/anthill23_rmats
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib

python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py \
 --b1 b1.txt \
 --b2 b2.txt \
 --gtf gtf/Homo_sapiens.GRCh37.87.gtf \
 --od bam_test \
 -t paired \
 --readLength 50 \
 --cstat 0.0001 \
 --libType fr-unstranded

</code>

==== performance tests ====
None. At this time.
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