which file should I use for generating beta-diversity?

I am not sure which table to use for generating the beta-diversity plot. I went through the qiime2-dada2 pipeline and generated two asv tables.
The first one is the table.qza file right after the dada2 step.
The second one is one of the tables I generated after I ran the " qiime taxa collapse" command. This the for loop code I used:
for i in {1..7}

do

qiime taxa collapse \

--i-table table.qza \

--i-taxonomy taxonomy.qza \

--p-level $i \

--o-collapsed-table table-L$i.qza

From my understanding, the first table doesn't have the OTU ID assigned yet.

The second table did have the OTU ID assigned. (I used the table at the species level)

This two tables generated two different beta-diversity plots, when I use the R package-vegan.

My question is which one I should use for generating Beta-diversity plot?

Thank you so much!

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Hello again,

I would recommend using the full table made by DADA2, as that includes all ASVs and no database bias.

Once you collapse by taxa level, you group ASVs together based on what the taxonomy the database can resolve, and add database bias: 100s of ASVs may get grouped into a single taxon like p__Bacillota, c__Bacillio,__Lactobacillales; f__? and all this variation at the ASV level is lost.

A summarized taxonomy table that only goes to order or family can be helpful for making bar plots, but I would use the :sparkles: original, maximum resolution ASVs :sparkles: for my beta-diversity calculations and PCoA plots.

P.S.

That table does have a feature ID (in the first column called "#OTU ID") and taxonomy if you have run a classifier, but the full ASV IDs are shown.

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Thank you so much for answering my question. This is very helpful

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