HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. It is developed by Simon Anders at EMBL Heidelberg.

References:

• https://academic.oup.com/bioinformatics/article/31/2/166/2366196

• http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour

• Module Name: htseq (see the modules page for more information)
• Example files in http://www-huber.embl.de/users/anders/HTSeq/HTSeq_example_data.tgz

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load htseq
[user@cn3144 ~]$ htseq-count input.sam input.gff

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. htseq.sh). For example:

#!/bin/bash
set -e
module load htseq
htseq-count input.sam input.gff

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] htseq.sh

Create a swarmfile (e.g. htseq.swarm). For example:

cd dir1; htseq-count input.sam input.gff
cd dir2; htseq-count input.sam input.gff
cd dir3; htseq-count input.sam input.gff
cd dir4; htseq-count input.sam input.gff

Submit this job using the swarm command.

swarm -f htseq.swarm [-t #] --module htseq