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Old 05-09-2016, 09:07 AM   #15
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Location: CT

Join Date: Apr 2015
Posts: 241

sequencing pcr dups isn't good because there is going to be a strong phylogenetic signal in that bias-the "universal" primers aren't perfect matches to all bacteria, so groups that match better will likely amplify quicker which will inflate their abundance. This is one of the big caveats to microbiome sequencing. Excessive sequencing depth doesn't make the problem worse but it can lead to a false sense of strength of your findings and it's expensive.
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