Community matrix csv for sample X feature

I want to compare communities from three separate analyses in R and was hoping I would be able to export a community matrix csv of feature relative abundance X samples (identical to the makeSequenceTable() output in DADA2).

Is there a way to obtain this table in Qiime2 from the table.qza and rep-seqs.qza?


Hello Caroline,

You can export data from a qiime file using one of the commands on this page:

That should give you the .fna file you want. Once you also have the .biom file, you can convert it into the the .tsv format using the commands on this page.

Is that what you are trying to do?


P.S. Once you have the .biom file, you can import it directly with Phyloseq and go crazy!


That is exactly what I am looking for! Thank you!

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