How to build an OTU table

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Hi @neocat,

This is intended. If you work through the tutorials again, you'll notice that the feature-table (i.e. the counts table) is kept as a separate file from the taxonomy. I suggest reading through the :qiime2: overview, for more details.

If you'd like to take a quick look at an old-style QIIME 1 like table, you can run the following commands:

qiime feature-table transpose \
    --i-table table.qza \
    --o-transposed-feature-table table-transposed.qza

qiime metadata tabulate \
    --m-input-file table-transposed.qza \
    --m-input-file taxonomy.qza \
    --o-visualization counts-and-taxonomy.qzv

Then view the counts-and-taxonomy.qzv on QIIME 2 View.

Protip: you can add multiple --m-imput-files as long as they share a common ID.

-Cheers!
-Mike