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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:
BioContainers: https://biocontainers.pro/tools/htseq
Home page: https://github.com/htseq/htseq

Versions

  • 2.0.2

Commands ~~~~~~~ - htseq-count - htseq-count-barcodes - htseq-qa - python - python3

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=htseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load htseq/XXXX ### you can run *module avail htseq* to check all available versions