My aim is to get a file with: the name of each read and the corresponding OTU it has been clustered in. I want this even for redundant reads, and I want the original name of the reads.
My idea is to use
deunique.seqs(fasta=, name=). So I’ve been trying to keep my name file at each step. But at the
pre.cluster(fasta=, name=) step I can’t keep it. I’ve seen this issue : How to generate precluster.names file in v1.42.0? · Issue #616 · mothur/mothur · GitHub with the same problem, but no solution to end up with a correct name file. Is it impossible to get a name file after the
pre.cluster step ?
If so, is there another way I can achieve my aim ?