HTSeq

Introduction

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

For more information, please check its website: https://biocontainers.pro/tools/htseq and its home page on Github.

Versions

  • 0.13.5

  • 1.99.2

  • 2.0.1

  • 2.0.2

  • 2.0.2-py310

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

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 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