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

Join Date: Apr 2015
Posts: 243
Default

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.
thermophile is offline   Reply With Quote