Problems in gff

[mpovidlov1]

I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3 It looks like the file contains multiple problems, mostly touching exons with introns of size 0. I can send examples

[mpovidlov1]

@snurk ?

[skoren]

The annotations come from liftoff/CAT so this is more a question for @mhaukness-ucsc or @diekhans Are these similar to issues asked in #31 and #37?

[mpovidlov1]

Thanks. The other issues mention other problems with earlier versions of the annotation files. Mine is quite specific. The records define exons like this (start end): 100 200 201 300

which means that the intron between them is of size 0

[mhaukness-ucsc]

Hi @mpovidlov1, could you please provide some examples? I think this is likely a result of errors present in the original GENCODE annotations, but I'll look into it.

[mpovidlov1]

Here is an example of the first problematic gene, starts on line 12:

[problems.txt](https://github.com/marbl/CHM13/files/8455851/problems.txt)

	111903	112896	transcript	-
	111903	112498	exon	-
	111940	112498	CDS	-
	111940	111942	stop_codon	-
	112499	112896	exon	-
	112499	112877	CDS	-
	112875	112877	start_codon	-

I have a list of more than 200 problematic genes referenced by line number (attached)

[diekhans]

Issue moved to CAT repo: https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/285