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

Join Date: Apr 2015
Posts: 239
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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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