Purdue University

Commands

• mageck
• mageckGSEA
• RRA

Module

You can load the modules by:

module load biocontainers
module load mageck

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 mageck on our clusters:

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

module --force purge
ml biocontainers mageck


mageck count -l library.txt -n demo \
     --sample-label L1,CTRL \
     --fastq test1.fastq test2.fastq

mageck test -k demo.count.txt \
     -t L1 -c CTRL -n demo