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@daniel-munro daniel-munro released this 31 Aug 00:51
· 16 commits to main since this release
v1.2.0
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Learn about vigilant mode.

Expands compatibility with GTFs from sources beyond Ensembl. Phenotyping should now also work with Gencode and RefSeq GTF files.

The calculation of exonic to intronic read ratio has also changed, both to work with non-Ensembl GTF files and as a theoretical improvement:

  • Instead of reporting exons found in at least a certain percentage of isoforms, report regions that are covered by exons in at least a certain percentage of isoforms. That allows, e.g., a region to be included if some isoforms have exons that extend beyond the region. Before, exon boundaries had to match exactly across isoforms after filtering by Ensembl-specific annotation sources.
  • Intronic regions are defined as regions within the gene (as defined by exons) that contain no exons in any isoform.
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