How do you work with non-assembled reads with "virus" signal?

Guillermo Domínguez Huerta @Guillermo-Dominguez-Huerta

03 June 2019 1 6K Report

Hi all,

I'm working to extract RNA virus sequences from metatranscriptomic datasets.

I observed that it is possible to detect some "virus" signal from non-assembled reads (by translation and hmmsearch) ... those that never get assembled....

Any of you know a way to deal with these reads that never get assembled?

Thank you,

Guillermo

Brian Hanley

Start with looking for hits on known viruses. Find some known viruses to use as templates for reads. And look at the workflow of the RNAseq system, because they use virus components, so you'll have false positives from that.

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