Sure you can, and sounds reasonably in your case. The reads that come from the RNA-seq experiment can be mapped not only to the reference genome (potato in your case), but the same reads can be also mapped to the genome of virus(es). Then you can have a look at the coverage of reads on the viral genome - and understand it as "viral gene expression". Do the viewing of reads mapped to the viral genome eg in IGV browser, this will give you an insight of what viral gene structures are really expressed.

From my experience: be prepared that the virus sequence (from eg. a database) that you expect to see is not exactly the virus that is really present in the experiment. Try the mapping with various strains - the mapping to a small viral genome does not take much time, so you can experiment , eg with the mapper settings. It may happen to be a bit messy, but there are good chances that you will find what you need.

In theory, you can try de-novo then with the reads not mapped to the potato and with the confirmed viral fragments as scaffolds - but have not tried this approach yet.

Anyway - good luck! :)

Sure you can, and sounds reasonably in your case. The reads that come from the RNA-seq experiment can be mapped not only to the reference genome (potato in your case), but the same reads can be also mapped to the genome of virus(es). Then you can have a look at the coverage of reads on the viral genome - and understand it as "viral gene expression". Do the viewing of reads mapped to the viral genome eg in IGV browser, this will give you an insight of what viral gene structures are really expressed.

From my experience: be prepared that the virus sequence (from eg. a database) that you expect to see is not exactly the virus that is really present in the experiment. Try the mapping with various strains - the mapping to a small viral genome does not take much time, so you can experiment , eg with the mapper settings. It may happen to be a bit messy, but there are good chances that you will find what you need.

In theory, you can try de-novo then with the reads not mapped to the potato and with the confirmed viral fragments as scaffolds - but have not tried this approach yet.

Anyway - good luck! :)

Washington:

I agree with Michal. You can use RNA seq for looking at quasi-species of PVY in potato. PVY is naturally polyadenylated, so you can make your RNA seq libraries enriching for poly-A RNA. For mapping, you can use the wild-type PVY sequences as your reference. I have done similar experiments with PMV in Brachypodium, and worked well. Another browser that might be useful for viewing the RNA-seq data is IGB. http://bioviz.org/igb/.

Good Luck!

Thank you guys.