#23 Counting reads on introns

[Marco]

Hi,

I am wondering if there is an easy way to use HTSeq (in particular HTSeq-count) to perform a read counts on gene introns rather than exons.

Do you have any hints?

Thanks a lot

Marco

[Smitha Shankar]

You could just modify the GFF file to have the coordinates of the intron instead of the exons.

[Simon Anders]

The new documentation (due to come online soon) will have more details on how you can write your own scripts for such specialized counting tasks.