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Old 05-09-2016, 08:49 AM   #13
Senior Member
Location: CT

Join Date: Apr 2015
Posts: 239

You need to rarify all of the samples that your are analyzing together to the same depth. Even if you are sequencing close to saturation, you can never know if a zero is truly absent from your community or simply not captured.

On your broader question I think 100k is pretty excessive for microbiome and you're likely sequencing a lot of PCR duplicates. (remember a decade ago we were looking at communities with 50-100 clones and in general finding the same broad patterns. More samples will likely give you more insight to your question than more sequences per sample)
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