It would be nice if there was a command that would be able to merge 2 metadata files from different studies. It could check for the columns that aren’t present in both and fill the samples that didn’t collect this information with a null value, such as “not collected”. Then, if column headers match, just add the values from the samples from the other study. It would make running meta-analyses in Qiime2 much easier for users.
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Hi @Stephanieorch,
Neat idea! We have an open feature request describing this issue, and discussing the current limitations (namely, 
does not have a metadata output type).
In the mean time, qiime1 has a method to do this.
I hope that helps!
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Also, metadata tabulate will merge metadata and allow you to download the merged TSV from the viz, but it only supports the INNER JOIN operation at the moment — useful for samples from the same study, but not helpful when combining studies.
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