Hi there,

Recently I did some analysis for ribosome depleted RNA_seq data. I also got the corresponding mRNA-seq data. When I loaded these two dataset into IGV. There are significantly more reads in intron compared to mRNA-seq data. In this case for ribosome depleted RNA_seq, I can still tell the exon structure based on the read coverage. Please see the snapshot I got from IGV. But I also had some data, I can't even tell the exon structure based on read coverage.

Here are my questions: 1) Could someone tell me the potential reason of these intronic reads? The reason I think of is introns that have been spliced out, degraded transcripts. 2) If there are intronic reads, does this mean there are reads come from degraded RNA fragments? If so, will this affect the downstream analysis, like DEG identification? 3) Is there anything that I should be very careful when doing analysis on such data?

Thanks, Shaojun