I just ran the cluster command using the output from my pairwise.seqs command. Here is the command that I used:
cluster(column=final.dist, count=final.count_table, method=nearest, cutoff=0.03)
And then I get the following output:
The annotated workflow that I’m following states that my output should be: “final.nn.unique_list.” instead. This is a problem, because when I opened the large .cons file containing all my OTU’s and samples, it seems like there is a massive overlap in taxonomy. If it were “unique”, I’m assuming all the taxa names would have been unique. I am a bit lost on how to fix this issue.
Many thanks in advance!