I am a master candidate in China and now enjoying Mothur in analysis my 16S rRNA V6 data. I have just meet a problem about OTU clustering. When using the following command,the cluster result file XXX.unique.an.rabund and XXX.unique.an.sabund gave me only the “unique” OTUs abundance.
dist.seqs(fasta=XXX.unique.fasta, cutoff=0.25, processors=8)
cluster(column=XXX.unique.dist, name=MetatongueRun4.names, method=average)
But in the Costello stool analysis example, *.an.rabund and *.an.sabund gave unique,0.00,0.01…0.07 OTU clustering results. My dataset XXX.unique.fasta contains ~88,300 unique V6 tags. Did the amount of my dataset matter to clustering? What should I do to get the larger divergence OTUs? (ps: When I tried the same commands on a smaller dataset containing ~5,000 unique V6 tags, the clustering command gave me unique,0.00,0.01…0.07 OTUs, just as the same to the Costello stool analysis example.)
Thank you very much.