Does rRNA depletion protocol give higher number of mapped reads in Intronic regions? Recently, I have downloaded a publicly available dataset, which are 350 tumor samples. I see the following information from the published paper.

They used Ribo Zero Gold and rRNA was depleted. Strand specific data. After aligning the data I did some alignment quality check with Qualimap RNA-Seq QC tool. I visualised the bam files in IGV. Alignment is good. For all samples 90% alignment rate was seen. I observed that in all samples Higher percentage of mapped reads were originating in Intronic regions. Followed by Exonic and intergenic regions.
I have seen a post here Reads mapped to exonic, intronic and intergenic regions where they say high intronic reads could be because of contamination. I googled about higher reads in intronic regions and found some papers Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion and some other links RIBO-DEPLETION IN RNA-SEQ – WHICH RIBOSOMAL RNA DEPLETION METHOD WORKS BEST? in which they said Greater intronic reads were with rRNA depletion protocol.
And even in this RNA-SEQ tutorial, it is mentioned that - A higher intronic mapping rate is expected for rRNA removal compared to polyA selection.
So, my question:
I am working with lncRNAs. So, I'm using the samples prepared with rRNA depletion protocol. Is this higher intronic rate is common in rRNA depleted dataset or do I have to check anything else to proceed further with these samples?
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.