otus and greengenes?

[MarwaTawfik]

@colinbrislawn

de novo, closed-ref, and open-ref clustering

Many thanks for your reply.
I didn't get the following comment fully; do you think I can pick OTUs (closd-ref) from denoised samples (that I ran dada2 on)?

De novo VS Closed Ref

No, I don’t think so. I’m not sure what the motivation would be to do that with OTUs. I could maybe see a use to do closed reference clustering for denoised sequence, which was done in the American Gut Manuscript to address some methodological issues. But, if you’re dealing with de novo OTUs and you have the raw data, why not just re-pick so you have consistent results?