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HTSeq Count

Part of the HTSeq package: counts reads covering specified genomic features

https://htseq.readthedocs.io/en/master/htseqcount.html

HTSeq is a general purpose Python package that provides infrastructure to process data from high-throughput sequencing assays. htseq-count is a tool that is part of the main HTSeq package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.

File search patterns​

htseq:
  - contents_re: ^feature\tcount$
    num_lines: 1
    shared: true
  - contents_re: ^\w+.*\t\d+$
    num_lines: 1
    shared: true