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how can I get the coverage over introns only in a RNA-seq experiment?
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12 months ago
Lila M • 470
UK

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!

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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.

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

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

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