Hello! I am running an alpha and beta diversity analysis of my ASV data. I rarefied my ASV data to the same read depth for Shannon Diversity Analysis, but I was wondering if I should use my rareified data for richness and Pielou’s evenness index as well as my beta diversity analysis where I run a PCoA. Thank you!
Hello!
If you first rarefied the feature table and then calculated Shannon, then you can use the same rarefied table for other metrics.
If you run core-metrics plugin within the qiime2, then you need to provide unrarefied table and indicate the sampling depth, so it will rarefy the table first and then calculate alpha and beta diversity metrics.
You also may take a look at qiime2-boots plugin that can perform bootstrapping instead.
Best,
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