ASVs generates more unassigned taxa rather than OTUs?

[Nicholas_Bokulich]

@TurboQiimer

is there scientific reasons for that?

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:

@Nicholas_Bokulich

This sounds like an issue with your reference database (incomplete? poor specificity?), the gene itself (lack of taxonomic resolution?), or the primers (poor specificity?). You should go back and check all three to troubleshoot. Provided the reference database fully covers your amplicons, the vsearch-based classifier in q2-feature-classifier should work well, so we can rule out the classifier.

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.