Difference in Exonic Mapping Rate - Qualimap vs RSeQC

[Chelsea McLean]

Hi all,

The Qualimap documentation says that "Exonic region includes 5’UTR, protein coding region and 3’UTR region." However, when we compare the genomic origin of reads calculated by Qualimap and RSeQC, we get different results and it appears that UTRs are not counted by Qualimap as exons. Has anyone else experienced this?

Thanks very much for any input!

Chelsea