Purdue University

Commands

• htseq-count
• htseq-count-barcodes
• htseq-qa
• python
• python3

Module

You can load the modules by:

module load biocontainers
module load htseq

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 HTSeq on our clusters:

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

module --force purge
ml biocontainers htseq

python -m HTSeq.scripts.count \
       -f bam input.bam ref.gtf \
       > test.out