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gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
MIT License
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Exons and introns coordinates #44

Open fgypas opened 4 years ago

fgypas commented 4 years ago

Hi

The .stats file, mentions a number of novel exons and a number of novel introns identified. Is there an easy way to get the coordinates of these regions?

e.g.
Novel exons:   16055/631658  (  2.5%)
Novel introns:    5926/381131  (  1.6%)

Thank you in advance Foivos

gpertea commented 4 years ago

Not precisely, at the moment, unfortunately. But you can glean some info about the transcripts owning those novel introns or exons by looking at the "class codes" provided in the output .tracking or annotated/combined gtf in order to select "novel" transcripts, if needed - for example a transcript with class code 'j' is likely to be a novel isoform so it involves novel introns (and novel exons too) though those overlap known reference introns/exons (yet they are still counted as "novel" since they don't exactly match reference intron/exon coordinates).

fgypas commented 4 years ago

Thanks a lot for the quick response. I think this would be useful for others as well.