ribosomal RNA removal

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4.3 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!

rna-seq • 1.2k views

ADD COMMENT • link updated 4.3 years ago by GenoMax 147k • written 4.3 years ago by storm1907 ▴ 30

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

ADD REPLY • link 4.3 years ago by rpolicastro 13k

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

ADD REPLY • link 4.3 years ago by storm1907 ▴ 30

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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 REPLY • link 4.3 years ago by rpolicastro 13k

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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 REPLY • link 4.3 years ago by GenoMax 147k

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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 REPLY • link 4.3 years ago by newbio17 ▴ 360

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