calculate Euclidean distance with same depth for the samples

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.
Zhan Gao

Welcome to the forum, @zhgao62!
qiime diversity beta doesn’t perform any kind of normalization, but qiime feature-table rarefy will let you

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.

Chris :badger:


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