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