I want to create a classic otu table. I have read some discussion on the forum, e.g How to make classic otu table with QIIME2? and exporting and Basic questions regarding classic OTU table in QIIME2. but the problem is that if we want to have taxonomic names we should collapse the data. when we collapse the table. qza or taxanomy.qza file we should determine the level for them so I think the result is not comprehensive for all asv’s, and the values are less.
is there any way to have a classic otu table with a more comprehensive results?
Not quite. If you want a feature-table that has taxonomic names instead of hashed-ids then yes you need to collapse (which has the limitation you spoke of force-collapsing OTUs down to higher levels). But this is not necessary, you can just keep the OTU table as-is, with the features-ids being unique identifiers, the same way you would with an ASV table, and have a separate taxonomy artifact that is called on whenever you need a taxonomic assignment.
Thank you, Dear, @Mehrbod_Estaki