HTSeq¶

Description¶

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. See the Scripts section in the overview documentation for what is available. Aavailable binaries: * htseq-count - This script takes an alignment file in SAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. * htseq-qa - This script take a file with high-throughput sequencing reads (supported formats: SAM, Solexa _export.txt, FASTQ, Solexa _sequence.txt) and performs a simply quality assessment by producing plots showing the distribution of called bases and base-call quality scores by position within the reads. The plots are output as a PDF file.

Environment Modules¶

Run module spider htseq to find out what environment modules are available for this application.

Environment Variables¶

HPC_HTSEQ_DIR - installation directory
HPC_HTSEQ_BIN - executable directory

Categories¶

biology, ngs