I would like to work out which of my Ribo-seq reads map to UTRs, but haven't been able to find any annotation files (GTF/GFF3) including UTRs or ORFs.
I was hoping to align my FASTQ reads against a Gencode.v30 reference, then take the SAM file and use htseq-count on it with a Gencode.v30 GTF/GFF3, but it looks as if those annotations don't include UTRs/ORFs. Have I misunderstood anything?
I would love if anyone could provide me with some pointers! I'm so sorry if I haven't found a piece of germane documentation. I've searched around a lot and can't find any tips.
Thanks so much.