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Does HTSEQ output include non-coding genes also?

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

htseq rnaseq ngs c.elegans worms
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updated by WouterDeCoster WouterDeCoster • written by s.singh • s.singh

1 answer

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.

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written by WouterDeCoster WouterDeCoster

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