16S rRNA de novo otu picking analysis

Question

[dcron13]

I have been attempting to create a 16S rRNA analysis pipeline that uses de novo otu picking, using mostly Qiime. The pipeline that I am using does not ever output the actual Greengenes identifiers that are referenced when assigning taxonomy to my otus that are defined. Is this standard in de novo otu picking? For some functional as well as some tree creation, I would need those Greengenes identifiers, so does this mean that to do analyses, such as PICRUSt, that I would have to do an open reference otu picking method?

Answer 1

[5heikki]

How could you get GG ID's with de novo OTU picking since reference is never used? You're picking OTUs de novo. And yes, you would have to use closed or open reference OTU picking to get the identifiers. Alternatively, I imagine you can somehow assign IDs to your de novo OTUs post OTU picking.