Recognize rRNA remove protocol from gene expression profile

Question

[Niek De Klein]

We have a large amount of samples for which we don't know the protocol that was used to extract the RNA. We want to know which samples were processed using the Poly-A selection protocol, and which with the Ribo-Zero-Seq protocol. Is there a tool available that can do this?

[Martombo]

I think tRNAs are the most useful thing you can look at, since they would not be taken up by poly-A selection but they would not be removed by ribo-zero protocols.

Answer 1

[5heikki]

If it's a metagenomic sample and ribo zero was used, then if you screen the sample for SSU rRNA, you'll find that the relative abundance of archaeal and eukaryotics SSU rRNAs is very high in relation to bacterial SSU rRNAs.