I am running OTU analysis based on MiSeq data. Since the final unique reads are so big: 176199 total reads, I used cluster.split() to bin them into OTU, so I ended up with 22441 OTUs. I want to perform UniFrac analysis based on OTU count table and OTU phylogenetic tree, so I will have to generate a phylogenetic tree from the representative OTU reads. And I was glad to find out that get.oturep() is available for me to extract the representative OTU. However, I am stuck at this step too, because the cluster.split() command didn’t produce a distance matrix to feed into the get.oturep command. All I have is a list file.
Could you please provide a way/command to extract representative OTU from what I have now?
I have a list file, OTU level shared file, final unique fasta file, and count_table file.