Hi,
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.
Thanks,
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 
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