I'm trying to figure out if there's anything wrong with my htseq-count result. I started with a sam file converted from a name-sorted bam file, then use the following options:
python -m HTSeq.scripts.count -m intersection-strict -s no -r name $nsorted_aligned_sam $refGtf
Htseq-count ran fine and showed that there were:
32268229 SAM alignment pairs processed.
When I looked into the count result:
Is this too high of a number of no_feature? I checked that the gtf file has the same chr formatting as the sam file, and that the stranded option is correct. Am I missing something here?
Any idea is appreciated. Thanks in advance!