Entering edit mode
3.7 years ago
storm1907
▴
30
Hello, I was asked to write a script for ribosomal RNA removal from viral RNA NGS data. I don't see the point to that, because how can there be ribosomal RNA sequenced with primers, specific for virus? Or I just do not understand something? Thank you!
How did they prepare their RNA for sequencing, and what type of sequencing did they perform?
Ī guess, casual RNA extraction and BGI library prep for one, specific virus - cov2.
You need to know how they collected and sequenced their RNA to know if any prepossessing steps are required. Right now there isn't enough info to give specific advice.
rRNA could be coming from host cells. You obviously need to find out /give us more information about the experiment.
If you are interested in just SARS-CoV-2 sequences then it may be simpler to isolate those and leave the rest behind.
I've had instances where faulty ribo-depletion kit during library prep for RNA-Seq led to presence of rRNA. I'm not sure if it's the best way, but if you have already performed alignment and have access to a
.bedfile for rRNA genes, you can try to usesplit_bam.pyfrom RSeQC.