Alpha rarefaction plotting issue

–p-max-depth in the command?
means max. frequency or max. number of sequence count?

Alpha rarefaction works with sequence counts. So for example, you could pass --p-max-depth 10000.


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As a note, in QIIME 2 we use more consistent terminology. So you’ll always see frequency for counts and relative frequency for proportions to a whole. I know QIIME 1 sometimes mixed terms a little bit, which can lead to confusion.

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