Hi @Lu_Yang! Unfortunately @colinbrislawn’s suggestion is incorrect w.r.t. DADA2 — it would be a bad idea to run merged sequences through DADA2 as single-end reads (it sounds like that is your plan), because DADA2 operates on the forward and reverse reads separately, then merges the reads as part of the denoising process. You could take @colinbrislawn’s advice if you wanted to run your reads through q2-deblur instead of q2-dada2 (as single-end reads). At this point though, it might be best to wait for 2017.11 to come out, which has official support for joined reads. Thanks!
1 Like