asgal
Link to section 'Introduction' of '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.
Docker hub: https://hub.docker.com/r/algolab/asgal and its home page on Github.
Link to section 'Versions' of 'asgal' Versions
- 1.1.7
Link to section 'Commands' of 'asgal' Commands
- asgal
Link to section 'Module' of 'asgal' Module
You can load the modules by:
module load biocontainers
module load asgal
Link to section 'Example job' of '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