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Old 06-11-2013, 04:14 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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One relatively straight-forward way to attack this problem would be to make a combined fasta file for the viral genomes and cassava and then map the transcripts/transcript fragments against it. You can then get an idea how likely each fragment is to come from the host or virus. I assume that tophat or something like that would be an appropriate aligner, since presumably you have a mixture of host (i.e. spliced) and viral (I assume transcripts would be single exon, but I've only made viruses, not studied them) reads and not doing so might bias things.

I should note that I've never done what you're trying to do, but if no one replies with a better idea then this is enough to get you started.
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