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v0.1.0 - stable version with complete docs
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@sreichl sreichl released this 15 Jan 13:23
· 25 commits to main since this release
v0.1.0
70c6c93

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

features

  • processing
    • BAM files of the same group are merged and indexed using samtools.
    • A bigWig file per merged BAM file is generated using deepTools::bamCoverage.
    • Information per requested gene from the 12-column BED file is retrieved (not necessary for genomic regions).
    • coordinates from the 12-column BED file are extracted and extended at the start and end by the configured parameter.
    • the number of isoforms i.e. number of lines in the BED file is determined (only for genes, for genomic regions it is hardcoded to 1) to plot below the tracks.
  • visualization
    • generate one plot per category of bigWigs and gene/region with the determined gene parameters.
    • generate one plot including ALL categories per gene/region.

documentation

  • complete documentation of used software, all features, and methods
  • external resources
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