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Old 04-22-2015, 01:03 AM   #3
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

@kaps: As Devon has already pointed out, your "reference" in this case is the fasta format genome file that you used to create your aligner indexes. You can't identify the "virus" hits unless you know (from an annotation source e.g. a GTF file) where the "virus" is in this reference genome file.

Where did you get your reference genome from? Perhaps there is an annotation file available there.
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