I have run two different sequences, performed DADA2 separately and merged them together as described in qiime2 documentation (same DADA2 parameters ).
I have got strange results- the microbial population between the two runs are very different. Samples that were sequenced together are tend to be much more similar compare to samples from the other run. It has no biological explanation, the origin of the samples is the same.
What can be the problem ? can it be a technical issue?
Thanks a lot