8000 all input transcript attributes and features should be preserved in annotation mode · Issue #82 · gpertea/gffcompare · GitHub
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all input transcript attributes and features should be preserved in annotation mode #82

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gpertea opened this issue Oct 11, 2023 · 0 comments
Open

all input transcript attributes and features should be preserved in annotation mode #82

gpertea opened this issue Oct 11, 2023 · 0 comments
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gpertea commented Oct 11, 2023

Currently only the basic exon structure and some basic GTF tags are preserved when gffcompare is running in "annotation mode", where a single input transcript file is given (+ a reference annotation) and no merging of input transcripts is requested - and thus the output GTF is named with the prefix .annotated.gtf

Proper implementation would make the "annotation mode" much more useful than it currently is. Issues to keep in mind:

  • CDS features must be fully preserved
  • --no-merge option should be automatically activated by default ?
  • handle GTF tag collisions for the added tags (at least warn about them; better yet: provide renaming options)
@gpertea gpertea self-assigned this Oct 11, 2023
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