How to make classic otu table with QIIME2?

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Hi @puritan,

The table.qza which you would have used to create the table.qzv will contain the table you are looking for (though you might have to transpose it to the orientation you want. Can’t remember from the top of my head). You can see the exporting tutorial to see how you can export the biom version of this file. If you want the table in another format lets say a .tsv then you can use the biom convert option on the new .biom file.

biom convert -i table.biom -o table.tsv --to-tsv

Keep in mind that this feature table will have the sequence variant unique ID as its identifier and not taxonomy. If you want the taxonomic names instead you’ll have to do assign them before exporting which needs the taxonomy.qza artifact (if you’re following the moving pictures tutorial).

For this step you can use the qiime taxa collapse function:

qiime taxa collapse \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 6 \ # or whatever level of taxonomy you want
  --output-dir taxtable/

Then you can follow the exporting directions as above.
Hope this helps!

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