htseq-count actual reads number is different with the result.

Question

[fhs.genomics.core]

dear all,

I met a case about htseq-count, the commend I used is following, htseq-count -f bam -i ID -t transcript -m intersection-nonempty -s no name-1515.bam Mus_musculus.GRCm38.gff >name-1515.paired.bam.read_count

but after I check the result,I find that some region have a lot of reads, but the count number is small. before I do htseq-count, read quality had be filtered, all is more then 30. like the fig show, the region marked is more then 2000 reads, but result shows 77 reads.

can anyone tell the reason. thanks

enter link description here

Answer 1

[fhs.genomics.core]

[Devon Ryan]

Please run it with the -o option and see why it's excluding the reads. It's likely doing this for a good reason.