Combine subsets of samples from different runs

Hi Timur
I have slightly different situation.
Run 1: Project A (30 samples) + Project B (45 samples) + Project C (30 samples)
Run 2: Project B (30 samples) + Project D (60 samples).
What would be the best strategy to combine Project B samples from two runs

  1. qiime mport fastq files for Project B from two runs into one qza file and subsequently process thru DADA2? OR
  2. Process both runs separately thru DADA2, filter table.qza and rep-seqs.qza samples for project B from each run, merge project B table.qza from two runs and perform subsequent analysis.

Hi @kindergarten ,
Hope you don't mind that I moved your question into new topic since it is a bit different from the original post.
But you already found the right answer as a second option:

I can only add that Dada2 parameters should be identical. It is recommended to denoise the whole run instead of the subset of samples since incomplete run may influence error-learning step in dada2 and results can be different.


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