Which files to use in q2-picrust2 pipeline?

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Hi @basil0125 ,

Thanks for taking the time to read through all the tutorials/docs first!

The way I see it, you have a couple of options here:

  1. Use your phyloseq table directly into the stand alone PICRUSt2 tool, that way you don’t have to worry about importing into Q2. This tutorial here should be able to help you export your phyloseq data out of R, note I haven’t tested the code myself though. Importing dada2 and Phyloseq objects to QIIME 2 . The added bonus here is that, currently, q2-picrust2 only works with version <2019.10 so you’d have to install an additional older version of QIIME 2.
  2. Use the original .qza files you have in QIIME2 with q2-picrust2 without filtering. I don’t think some filtering is going to have a significant effect on your PICRUSt2 analysis. In fact, to save you computational time/resources I would even recommend doing some filtering on your qiime2 tables first, so matching your phyloseq filtering seems like a good idea. Take a look at this tutorial for the various ways you can filter your qiime2 table: Filtering data — QIIME 2 2021.2.0 documentation
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