how can I get the coverage over introns only in a RNA-seq experiment?

Question

[Lila M]

Hi everybody, I've just wondering the best way to get the coverage over introns (only) in RNA-seq experiments (human genome) My first approach is to download the complete intron list from UCSC. Then I could get the overlaps (using bedtools intersect or samithing similar) with each bed file. Once I get that, I may create a coverage profile using computeMatrix (deepTools). But I'm not 100% if this is totally right. I appreciate if someone has done this before and would like to share! Thanks!

[ATpoint]

There are plenty of posts out there about getting exon coverage. You can do the same just with introns as reference. I am not sure if UCSC has intron lists ready, but you can follow my tutorial to get them from any gtf/gff file.

[Kristoffer Vitting-Seerup]

Do you want to create coverage plots or count the number of reads mapping to exons?

[Lila M]

both , coverage plot and number of reads mapping to INTRONS will be nice :)