Does HTSEQ output include non-coding genes also?

Question

[s.singh]

Hi Everyone,

For C.elegans, the HTseq output files have 46,779 genes (WB gene names). Worms should only have ~20,000 coding genes. Does anyone know why we have 2x more genes in our output? Does this include non-coding genes?

Thanks S

Answer 1

[WouterDeCoster]

HTSeq count will output anything which is in the annotation file when you use it. You could therefore have a GTF/GFF which has non-coding genes.