kissplice2refgenome
Link to section 'Introduction' of 'kissplice2refgenome' Introduction
KisSplice can also be used when a reference (annotated) genome is available, in order to annotate the variants found and help prioritize cases to validate experimentally. In this case, the results of KisSplice are mapped to the reference genome, using for instance STAR, and the mapping results are analysed using KisSplice2RefGenome.
Docker hub: https://hub.docker.com/r/dwishsan/kissplice-pipeline
Home page: https://kissplice.prabi.fr
Link to section 'Versions' of 'kissplice2refgenome' Versions
- 2.0.8
Link to section 'Commands' of 'kissplice2refgenome' Commands
- kissplice2refgenome
Link to section 'Module' of 'kissplice2refgenome' Module
You can load the modules by:
module load biocontainers
module load kissplice2refgenome
Link to section 'Example job' of 'kissplice2refgenome' 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 kissplice2refgenome on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=kissplice2refgenome
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers kissplice2refgenome