To whom this concerns, Been forging ahead regarding the use of QIIME2. One question, regarding merging runs that doesn't seem to be answered quite clearly. In our equivalent qiime1 merge, we would merge after the merging of joined_paired_ends.py (once we get the sequence.fna). But one thing I reme…

[image] ben: If we wanted to re-do with UCLUST tree-based closed or open picking, the merging of MiSeq files should be done prior to this step? correct, if you use dada2 or deblur, merge the feature table and reference sequences after denoising. for OTU picking, merging sequences is easiest …

DADA2 multiple sequencing runs - de novo picking allows for merging after artifact?