HTSeq

HTSeq is for high throughput sequencing data analysis. Covering everything from BAM file manipulation to counting reads this package is a helpful tool for sequence analysis. This module consists of htseq-count, htseq-count-barcodes, and htseq-qa. htseq-count accepts a list of alignment files and a gff file for input while outputting a counts file. htseq-count-barcodes is similar to htseq-count but is designed for SAM, BAM, and CRAM file formats.

For additional information and examples please refer to the documentation

Execution:

ml biocontainers htseq
htseq-count <alignment files> <gff file>

tip

This module loads several tools. To see what tools are available, run report_subtools.sh htseq

Parallel Capabilities: Single core default, Multithreading options supported.