Kissde

Introduction

kissDE is a R package, similar to DEseq, but which works on pairs of variants, and tests if a variant is enriched in one condition. It has been developped to work easily with KisSplice output. It can also work with a simple table of counts obtained by any other means. It requires at least two replicates per condition and at least two conditions.

For more information, please check:
Docker hub: https://hub.docker.com/r/dwishsan/kissplice-pipeline
Home page: https://kissplice.prabi.fr

Versions

  • 1.15.3

Commands

  • R

  • Rscript

  • kissDE.R

Module

You can load the modules by:

module load biocontainers
module load kissde

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 kissde on our clusters:

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

module --force purge
ml biocontainers kissde