Run qiime2 for multiple studies with different sample sizes


I have output from different studies of 16S amplicon-sequenced reads with different sample sizes. They are from either V4 or V3-V4 regions but I want to analyze them together. My question is:

  1. how can I analyze them together?
  2. can I run once qiime2 with all datasets?
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It depends what your question is but my initial thoughts would be to import and denoise separately until you have both sets merged into single end reads (but still ASVs not assign taxonomy). Then trim the V3-V4 region to the V4 region only and merge both datasets.

In theory you should also run samples from different sequence runs separately - although I don't know exactly how much difference that will make.

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