Hi all
First have to admit, I’m one of the greedy SOBs that Pat ranted about in his recent blog post, did miseq of v1-v3 using 300bp PE.
I’m guessing that this contributed to the fact that my dist file coming out ot the dist.seqs is ~400 gigs.
Number of unique seqs is 212996, total number of seqs:972645, so about 22% unique seqs (min length is 400bp, I used diffs=2 in pre.clust, this may have contributed to the inflated number of uniques but i digress).
I ran the dist.seqs with a cutoff of 0.20 (took it a week) and the cluster command with a cutoff of 0.03.
When I ran the make.shared command with 0.03 cutoff
I only get 0.01 cutoff and the file name is final.an.unique_list.shared
I wonder is this happening since I used a cutoff of 0.03 at the cluster stage and now 0.01 is the new 0.03, mothur’s actually giving me 3% dissimilarity otus but calling it 1% since this is all it has or are these legit unique OTUs?
Thanks in advance
Ido.