Is there a way to detect discrepancies in GFF files such as:
1- A gene has 3 transcripts, 1 is oriented on the forward strand, 2 are oriented on the reverse strand. I tried with Gffread, but it just affects the value of the first transcript met.
2- A transcript that's on chromosome #2 is associated to a gene that's on chromosome #1.
I've seen these situations on an official annotation from UCSC, so I wonder if there's a way to automatically detect and correct them. I've seen them using mikado compare, because it crashes when finding these situations. Maybe AGAT could handle that (I didn't find but I think it's worth asking) ?
Thanks for the help !
EDIT: AGAT actually detects discrepancies in
agat_sp_compare_two_annotations.pl. It outputs "We fixed 1 wrong level2 location cases" for the first case (transcripts oriented both ways). But can we output the corrected files ?