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wejlab / animalcules

R shiny app for interactive microbiome analysis
https://wejlab.github.io/animalcules-docs/
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Is Alpha rarefaction required? #46

Closed s6aamani closed 3 years ago

s6aamani commented 3 years ago

Hi, I have experienced that in diversity analysis done using qiime2, a rarefaction [normalization] step was recommended. However, in animalcules, no such step is performed. I am confused about whether rarefaction step is required or not. Will it change my result? Thank you

jasonzhao0307 commented 3 years ago

The rarefaction step is not necessary. Check out this paper - McMurdie, P. J., and Holmes, S. (2014). Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10:e1003531. doi: 10.1371/journal.pcbi.1003531