RNA-Seq quality control tool looking for number of aligned reads in different genomic regions

Question

Anybody aware of a quality control tool for RNA-seq data that is checking the ratio of number of reads aligned to coding exons of genes vs number of reads aligned to introns or intergenic regions.

Thanks for the help

Answer 1

I’ve used the featureCounts tool in R bundled with the Rsubread package. Assessing the quality of the sequencing can be highly dependent on the sequencing methodology, but you can easily compare intergeneic versus exonic, if that’s the metric you settle on.