Open karlaarz opened 2 years ago
Hi, I am not a GFFCompare developer, but I have just read your issue. In order to compare two GTF files, one of the two GTF files has to be specified as the reference annotation file with the -r parameter. Transcripts of the other file will be compared to transcripts in the reference file, and they will be classified depending on their relationships with reference transcripts (you can find class codes and their meanings on this GFFCompare documentation page in the section "Transcript classification codes": https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). I hope this helps, even if your issue is quite old now.
Hi,
I have two different gtf files (one created from short reads and the other from long reads), and I would like to compare them to see if any of the transcripts are similar among them. I am using the command:
gffcompare gof_filt.gtf gof_transc_in_flair.gtf -o gffcomp_short_flair_gof
However, the results of the
.tracking
file only have theclass_code 'u'
, and the stats are:I am not sure what can be wrong, as even the already annotated transcripts are tagged as "unknown" (
class_code 'u'
).Any help is appreciated!
Thanks