htseq
Link to section 'Description' of 'htseq' Description
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
Link to section 'Versions' of 'htseq' Versions
- Anvil: 0.11.2
Link to section 'Commands' of 'htseq' Commands
- htseq-count
- htseq-qa
Link to section 'Module' of 'htseq' Module
You can load the modules by:
module load htseq
Link to section 'Example job' of 'htseq' Example job
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 load htseq
htseq-count input.bam ref.gtf > test.out