I have followed the moving picture tutorial Qiime2. For functional genes, I have got many unassigned taxa. My friend who has used Qiime1 commented to me that "you should not have gotten such a result!2 As we know, Qiime2 produces ASVs via DADA2 and Qiime1 produces OTUs, would it be the case that I got higher unassigned taxa? If yes, is there scientific reasons for that? I would appreciate if you guide me.
Thanks a lot
No, probably not. This is probably either a user error or an error with your database. This is an issue I think I already described fairly well here:
So either your primers are no good (lots of non-target hits) or your reference data is no good (does not capture the full diversity for your functional gene target).
I think you should do some careful assessment of your reference database and primers before proceeding.