How can I create taxonomy table with frequency?


In “Moving pictures” tutorial, I would like to create the taxonomy table with frequency where I can see the frequency of each taxonomy (not as feature ID) for each sample in order to use that table (as biom or csv file) for further statistical analysis with R.
I thought I could get that data by exporting “taxa-bar-plots.qzv” because it was the result of combining frequency and taxonomy data, but I did not work.

Could you please let me know how to create that table?
Thank you and have a good holiday!

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Hi @scho73! You can use qiime taxa collapse to create a feature table of frequencies at a particular taxonomic level (this is similar to QIIME 1’s script). Once you have the collapsed feature table artifact, you can export a .biom file using qiime tools export.


Hi Jai,

It is working!
Thank you so much for your kind and quick response.

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An off-topic reply has been split into a new topic: How to make rarefied taxonomy tables at each taxonomic level?

Please keep replies on-topic in the future.

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