I have 16s paired end data that I’m trying to analyse but I’ve been struggling to define/understand the output from the vsearch command. This is my first time programming/using bioinformatics and my questions might be silly.
I’ve understood that you can either work with ASVs or OTUs so I tried both to see how they differ. To generate my FeatureTables and RepSeqs i did the following for the two:
ASV analysis - DADA2
OTU analysis - vsearch (de novo, 97%) with DADA2 input
Now my question is, if using OTU clustering with DADA2 input, doesn’t that generate a FeatureTable and RepSeqs that are some type of cross between OTUs and ASVs. To my understanding, with the vsearch command I’m clustering ASVs, which would mean I don’t get a classic OTU table? When using this method, to I refer to it being a product from ASVs or OTUs?
The diversity measurments varied between the ASV and OTU with DADA2 input and I wonder if it would vary if I made a third beta diversity with a classic OTU table?