why there is no gene_id, transcript_id in the example gff file given in .md file?

[corn23]

Hey Barrymoore, thanks for your detailed explanation for the gff format. I am now more clear about it. I have a small question though about the attributes. From http://mblab.wustl.edu/GTF2.html, I see there are attributes like gene_id, transcript_id while in the gff example in your .md file, there is only ID. Are they the same? Do we have a consistent standard form for gff file?

[cmdcolin]

Those belong to the gtf format, sometimes called gff2, but it is not part of gff3 at all.

[Juke34]

People often confuses GFF and GTF, I did a complete review of the two formats here: https://github.com/NBISweden/GAAS/blob/master/annotation/CheatSheet/gxf.md.