ASGAL

Introduction

ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation.

For more information, please check its | Docker hub: https://hub.docker.com/r/algolab/asgal and its home page on Github.

Versions

• 1.1.7

Commands

• asgal

Module

You can load the modules by:

module load biocontainers
module load asgal

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run ASGAL on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=asgal
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers asgal

asgal -g input/genome.fa \
    -a input/annotation.gtf \
    -s input/sample_1.fa -o outputFolder