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Old 01-11-2018, 05:59 AM   #2
Senior Member
Location: CT

Join Date: Apr 2015
Posts: 243

I don't know qiime well (only used enough to know that I strongly prefer mothur). So can't tell you exactly where to combine but you can't combine OTU tables if you do denovo clustering. In mothur, I combined after demultiplexing, sequence qc, and chimera checking but before aligning and clustering into OTUs
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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