Hi pernille.rainer

According to the HTSeq-count documentation, you can specify on what type of feature, you want to assess the counting:

-t feature-type, --type= feature-type

feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)

Thus if you use "-t gene", you should get all reads within a gene-locus (frankly, I haven't tested it).

Denote, that overlapping features will appear in this scenario more often and more reads will be "ambiguous" .

Cheers, Michael

It all comes down to which gtf you use as input. So if you gtf has intervals containing the entire gene or introns and exons separately, that will work.

That's what I though thank you :) But I don't know much about all that, where can I find a gtf containing entire gene or introns? I tried on ensembl but I were not so successful

Thanks!