Export/Extract Taxonomy by Feature


I am trying to export/extract a table that combines both my FeatureTable[Frequency], and FeatureData[Taxonomy], in a format that would allow me to conduct analysis outside of Qiime2. I am looking effectively for a copy of my FeatureTable, with Taxonomy as an additional field. I have tried exporting and extracting at different positions in the analysis, and am working an assumption that exporting following a qiime taxa barplot command - being the only point (I can think of) at which this information comes together, would allow me to access this information. However I can find no usable route having exported or extracted this file from Qiime2.

Could anyone point me towards a resolution?

Many thanks

1 Like

Hi @five!

We don’t have a simple way to export those artifacts together. But you should be able to export the FeatureTable and FeatureData[Taxonomy], then you can use biom directly to merge them together. @jairideout wrote some excellent instructions for accomplishing this in another topic.

Let me know if that meets your needs!


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