Entering edit mode
5.6 years ago
RiNG
▴
10
I am using qualimap to assess the quality of my alignments.
However for most samples I am having around 12% of intronic reads. I know for a fact I have no gDNA contamination. What is causing this to happen?
How about intergenic reads? Why is it bad to have 50% intergenic reads?
Perhaps this wasn't polyA enriched, in which case that would be quite reasonable.