picrust parameter in make.biom


I am using PICRUSt from mothur, and I just want to make sure I correctly interpret what I’m doing when I use make.biom. By including the picrust mapping file, I am effectively using “closed-reference” picking at my chosen OTU level (in this case 0.03), correct? I had all of my OTUs in my shared file that are classified against greengenes but without constraint, just as in normal SOP in mothur using SILVA, until I add the picrust parameter in make.biom, which collapses my OTUs into the reference OTUs? If this is not too bad (in my case this doesn’t seem to be too bad, I go from ~600 OTUs in the .shared file to 590 OTUs in the .biom_shared).

Many thanks!

I think your interpretation is correct. The one caveat being that many of your OTUs won’t classify to the genus level, so you’ll probably be stuck with family or higher levels.