I don’t completely understand why the cutoff changes in the cluster command after reading the FAQ (http://www.mothur.org/wiki/Frequently_a … eighbor.3F).
Can you explain: “If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03, because it’s not possible to merge at a higher level and keep all the data” in more detail? Why do you “lose data” when you start clustering at higher cutoff levels?
I am trying to create OTUs at multiple different sequence dissimilarity thresholds, from 0.00 to 0.25 at 0.01 (1%) increments. When I try and set the cutoff to 0.25 using the cluster command, it always changes the cutoff to 0.14. Is it possible to do what I am trying to do here (create OTUs with dissimilarity thresholds up to 30%)? If so, how should I go about doing this?
Thanks!