Software: ASGAL
Description
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.
Available Versions
Unspecified: | 1.1.7 |
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Docker hub: https://hub.docker.com/r/algolab/asgal and its home page on Github.
Commands
- asgal
Module
You can load the modules by:
module load biocontainers
module load asgal
Example job
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