Interesting question, @Magreet. I believe your understanding of qiime taxa collapse is correct, but I don’t believe this functionality is currently available in QIIME 2.
Big-picture, I suspect what you’re trying to do is:
- First, add taxonomic assignments to your original FeatureTable[Frequency].
- Second, join that table with the Feature detail table of collapsed taxa, joining by taxon.
This would produce a long-form table with N ASVs for rows, and columns for feature count, taxonomy, taxa count, and maybe counts per sample.
If I’m understanding your desired outcome correctly, I think it will take a bit of data manipulation. There are a bunch of different ways to go about this, and Python, R, whatever language you prefer are probably the best approach. You could use Excel, but I suspect it would be rather painful (and I love spreadsheets!).
Here are a couple of somewhat-related topics you might want to check out for bread crumbs: 1, 2.
Hope that helps,
Chris 