Entering edit mode
4.9 years ago
jpcchoy
•
0
Hi, everyone.
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.
Are you sure Gencode annotation doesn't include UTRs?
Yes! I had not noticed that h.mon, but you're absolutely right. Unfortunately, I've run htseq-count in the following way and all of my sequences map to 0 features...
All I get is this:
I got my sorted.bam from rsemoutput.transcript.bam, which I sorted with samtools sort. Any idea what might be going wrong? I haven't found any hint of what's going on in RSEM/SAMtools/HTSeq documentation, and would hugely appreciate any help.
If you want to count reads over utr region, try
featureCounts -t UTR -f
. I don't know if it will work, but its worth a shot.I just tried this a few times with different parameters, and every time I get a
Do you know why this might be?
Context:
And I can provide more details if helpful!