Hello everyone,
I am new to Mothur and would appreciate your help.
My request is very simple: I have samples of pyrosequencing data (about 30,000 reads per sample), and I want to find out the genera richness, i.e. how many OTUs there are at 95% similarity. What would be the easiest way to do that?
Many thanks in advance,
P.
Here you go…
classify.seqs(…)
phylotype(…)
read.otu(…)
summary.single(…)
Thank you for the answer, but I could not find in there where to set the % of dissimilarity. I neglected to mention that I do not wish to taxonomically define the sequences, ONLY to see how many OTUs there would be using 3%, 5%, etc.
The goal is to compare the richness given by the taxonomic approach (RDP classifier) to the richness given by OTU approach (MOTHUR).
Thanks again!
Ah, ok. Well that’s a hard question since we don’t have a real species definition, much less an species definition. The distance cutoffs are really just a guess. Once you get your sequences aligned, you should do the following…
dist.seqs(…)
cluster(…)
read.otu(…)
summary.single(calc=sobs-…)
This will give you the number of observed OTUs for each distance cutoff. Hope this helps.