Is there a way to filter out duplicate samples so I can merge feature tables without doing it outside of qiime2? How do you recommend removing duplicate samples run on both runs @thermokarst?
there is a way to filter out any kind of samples, duplicate or otherwise: qiime feature-table filter-samples. You can either pass in a sample metadata file that only contains samples you want to keep, or you can add a column to the full metadata file that indicates whether a sample is a duplicate or not (and hence whether it should be filtered by that command).
But there is also another way: use qiime feature-table group to collapse duplicate samples (e.g., taking the sum of their reads).
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