picrust parameter in make.biom

Commands in mothur
1

Hi,

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!
Beth

2

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.

Pat