Hi, now I'm studying how to handle RNA sequencing result. I have a question about "annotation". I made transcriptome using stringtie(with GTF annotation file) and analyze splicing patterns with GFFcompare.
My aim is compare splicing patterns between normal condition and knock down condition transcriptome annotated as "nonsense mediated decay" in gencode.annotation. So I mapped my result and ran Stringtie2 with custom annotation file(I picked especially transcript_type : "nonsense_mediated_decay). And I used GFFcompare.
But result was
I think all the transcripts which is not nonsense mediated decay target were sorted as "u"(unknown). So my question is how I can see difference of ratio of "u" in only NMD targets? How can I exclude unannotated transcripts before doing GFFcompare?