htseq
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'htseq' Versions
- 0.13.5
- 1.99.2
- 2.0.1
- 2.0.2
- 2.0.2-py310
Link to section 'Commands' of 'htseq' Commands
- htseq-count
- htseq-count-barcodes
- htseq-qa
- python
- python3
Link to section 'Module' of 'htseq' Module
You can load the modules by:
module load biocontainers
module load htseq
Link to section 'Example job' of '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
htseq-count input.bam ref.gtf > test.out