Dear Kelmer,
We do encounter the same issue. Almost 95% of our ASVs are not assigned to any taxonomy when analyzing ITS data using UNITE database.
I did not follow the same steps you did but followed this analysis pipeline. So I assume the problem arose in the last step- using UNITE to assign taxonomy.
Recently, I discovered a new reference data processing tutorial and applied it to 16S data. And also found this topic to apply the same approach to fungal data. This might be the solution to our problem but haven't tried yet.
Hope we find a solution.
Selin
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