Does rRNA depletion protocol give higher number of mapped reads in Intronic regions?
It's not so much that you have &quot;intronic contamination&quot; or &quot;genomic contamination&quot;, rather you're not selecting explicitly for full-length mature transcripts with rRNA depletion. That is the most common cause for higher intronic read rates. There's nothing you can do about this post-hoc, just continue along.
BTW, many lncRNA's are polyadenylated, so you'll keep them with poly-A selection.