Combining Datasets with 2 sets of Primers

[colinbrislawn (Colin J Brislawn)]

Good afternoon,

@jbethany

variations were causing identical sequences to be labeled separately

@Nicholas_Bokulich

but even a 1 nt difference is enough to cause two otherwise identical sequences (with 1 nt difference) to become separate features

This is true of the dada2 denoising algorithm; it's very sensitive to small biological differences, and also to small technical variation. The older OTU picking methods are much less sensitive to this; default of (97% similar == 3% diff) * 300 bp = 9 bp diff can be in a single OTU.

High precision methods may not be a good fit for a messy data set. Greedy heuristic clustering lacks accuracy and precision, but it's flexibility and tolerance make it a reasonable solution for funky data sets.

Colin