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Old 12-10-2015, 09:26 AM   #6
adam.geber
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Location: United States

Join Date: May 2014
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Can you describe your DNase treatment more thoroughly? Also, what size filters were you using? Viral-like particle enrichment is quite difficult and needs to be tailored to each sample type in order to get a high proportion of viral-origin reads.

How were you preparing libraries from your DNA extracts? Do you still have those samples? Also, what software are you using for taxonomic classification? Classification will depend entirely on what you're using as your reference -- can I ask what you're using for this as well?

Depending on your contig size you might be able to look for the colocalization of reads annotated as bacterial and viral within a single contig (although this could also be a sign of misassembly).
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