I want to use command “qiime diversity beta” to calculate Euclidean distance. My question is can I use this command to set the samples at the same depth and calculate Euclidean distance.
Subsample frequencies from all samples so that the sum of frequencies in each sample is equal to sampling-depth.
You could then run qiime diversity beta on your rarefied feature table. (This is how
qiime diversity core-metrics handles normalization. )
Is that what you were aiming for? If not, please clarify.
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