So I am clustering functional genes (not 16S) and I am trying to figure out which clustering percentage yields groups of sequences (let’s call them OTUs, for short) with the same function.
I followed the “moving tutorial” process, I used DADA2 for quality control and then I proceeded with clustering using the vsearch de-novo clustering method .The command I used for this is:
qiime vsearch cluster-features-de-novo
Now I want to see what sequences clustered together in an OTU. I.e., I have a list of representative sequences for each OTU, I want to see what other sequences belong to that OTU other than the representative sequence.
I have not been able to do this with Qiime nor Qiime2, but the usearch tool (natively) had an option to map all reads to the Representative sequences and create both a mapping file and an OTU table. Is there such an option with Qiime2?