Question: ribosomal RNA removal
0
gravatar for storm1907
9 weeks ago by
storm19070
storm19070 wrote:

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!

rna-seq • 154 views
ADD COMMENTlink modified 9 weeks ago by genomax91k • written 9 weeks ago by storm19070

How did they prepare their RNA for sequencing, and what type of sequencing did they perform?

ADD REPLYlink written 9 weeks ago by rpolicastro2.0k

Ī guess, casual RNA extraction and BGI library prep for one, specific virus - cov2.

ADD REPLYlink written 9 weeks ago by storm19070

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.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by rpolicastro2.0k

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.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax91k

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 .bed file for rRNA genes, you can try to use split_bam.py from RSeQC.

ADD REPLYlink written 9 weeks ago by newbio17240
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