CRwiki

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/ .

Below release of rMATS 4.0.2¹⁾ ( 04/25/2018 ) is described and used.

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

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
 

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software

Tools (written in C using htslib) for manipulating next-generation sequencing data. The original samtools package has been split into three separate but tightly coordinated projects:

    htslib: C-library for handling high-throughput sequencing data
    samtools: mpileup and other tools for handling SAM, BAM, CRAM
    bcftools: calling and other tools for handling VCF, BCF

Software and its description is available at : https://github.com/samtools/samtools
software instalation @anthill23

Before you can use samtools tools at anthill you need to install it.

Firstly login to anthill23.cent1.uw.edu.pl and open an interactive session :

srun -p short --pty bash -l

Then to prepare htslib run following commands (it will take less than 3 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/htslib
cd htslib
autoheader
autoconf
./configure --prefix=/home/users/${USER}/anthill23_soft/samtools/htslib
make -j ${SLURM_NTASKS}
make install

Then to prepare samtools run following commands ( it will take less than 4 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/samtools.git
cd samtools
autoheader
autoconf -Wno-syntax
./configure --prefix=/home/users/${USER}/anthill23_soft/samtools
make -j ${SLURM_NTASKS}
make install

Then to prepare bcftools run following commands ( it will take less than 3 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/bcftools.git
cd bcftools
autoheader
autoconf
./configure --prefix=/home/users/${USER}/anthill23_soft/bcftools
make -j ${SLURM_NTASKS}
make install

As a result samtools and bcftools binares will be located at :

/home/users/${USER}/anthill23_soft/samtools/bin
/home/users/${USER}/anthill23_soft/bcftools/bin

batch file template

First login to anthill23.cent1.uw.edu.pl.

Then create job file (batch), and save it as i.e. samtools_testrun.batch .

#!/bin/bash -l
#SBATCH --job-name=samtools_test
#SBATCH --partition=long
#SBATCH --ntasks=2
#SBATCH --mem 2048M

#samtools and bcftools binary executable paths
SAMTOOLSBINPATH=/home/users/${USER}/anthill23_soft/samtools/bin
BCFTOOLSBINPATH=/home/users/${USER}/anthill23_soft/bcftools/bin

#printout some info
echo "samtools at anthill test"
echo "date: " `date`
echo "node_name: " `hostname`

#run samtool
${SAMTOOLSBINPATH}/samtools

#run bcftool
${BCFTOOLSBINPATH}/bcftools

Then run created batch file ( value 60628 is jobID, it will be different in each job submission):

[anteater@anthill23 tests]$ sbatch star_testrun.batch
Submitted batch job 60634

Depending on availability of computing nodes your job should end in just few moments, and batch output will be located in slurm-60634.out file.