htseq counts on genes (introns + exons)

Question

[pernille.rainer]

Hello,

I was wondering if there was a way of using htseq to count the number of reads per genes (introns + exons) and not only on the exonic regions of genes.

Thanks a lot!

Answer 1

[michael.ante]

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

Answer 2

[WouterDeCoster]

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.

Answer 3

[pernille.rainer]

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!

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

The information you want is already included in a standard gtf file, see third column whenever it indicates 'gene'. You can use the -t flag in htseq count to specify which feature from that third column you want to use for counting.

[Devon Ryan]

Are you sure about that? Usually there are "gene" and "transcript" entries.

[WouterDeCoster]

I just had a look and at least in the gtfs of GRCh38.81 and GRCh37.82 a 'gene' and 'transcript' feature type is present.