My background is in environmental bacteriology so my apologies is this is a silly question...
I am trying to shot-gun sequence (Illumina/454) RNA viruses. So far I've been able to generate "high-quality" cDNA and from that "very nice" libraries for each of the platforms, but the resulting data is a bit crappy in that there's >99% host sequence resulting in low coverage of the target (viral) genomes. I'm wondering if there's a way (sucrose of CsCl gradient? biotinylated probes attached to magnetic beads?) that we can use to reduce the amount of host signature in the samples.
Preferably this method would use either a cell lysate (we receive them in Trizol) or extracted RNA, rather than an upstream process...but if need be that might be do-able as well.
Thanks in advance!
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Separation of viral RNA from host nucleic acids
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