Question: RNA-Seq: can one implicate viruses if unmapped reads map to virus sequences?
gravatar for jobinv
6.2 years ago by
Bergen, Norway
jobinv1.1k wrote:

This article seems to have an interesting approach; if I understand it correctly, they first map their human reads to the human genome, and then take the unmapped reads to find out whether they map to virus databases. If they do, then they seem to suggest that one could theorize that the virus could be implicated in the pathogenesis of the disease studied. Is this kind of conclusion warranted from such a finding?

virus rna-seq • 2.5k views
ADD COMMENTlink written 6.2 years ago by jobinv1.1k

Well, it's a first step. Obviously a lot of follow-up experiments and validation is needed to establish the link. As an initial screening step it is reasonable (and has been used many times by various groups).

ADD REPLYlink written 6.2 years ago by Mikael Huss4.7k

I haven't read the paper but is there an explanation why to use bowtie(2) and not tophat(2). AFAIK bowtie is not capable of resovling splice junctions. Therefore some amount of unmapped sequences will fall onto those...

ADD REPLYlink written 6.2 years ago by Phil S.660

True, or you could throw in filtering against a cDNA reference as well. Bowtie2 is much faster than Tophat2, maybe that's the reason.

ADD REPLYlink written 6.2 years ago by Mikael Huss4.7k

I am also trying to understand the pipeline used. They mention that it works with RNA-seq data. However, RNA-seq data will have all the introns spliced out. So what about that viral integration which occurred in the intronic region?

ADD REPLYlink written 2.8 years ago by KVC_bioinfo450
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