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one of the critiques against rarefaction is that you have to rarify to some arbitrary level of sampling coverage some arbitrary number of sequences to base your refraction on is that true not in my case i dont feel like its arbitrary maybe to someone outside looking in at what were doing they might say well you know whyd you say 3000 sequences that seems arbitrary in this episode of code club i am going to remove the mystery if there was a mystery i dont know about that but anyway were going to remove the mystery and im going to share with you my thought process for how i determine what number of sequences that i will rarefy my data to were going to use r were going to use some logic and im going to kind of give you some principles to go off of that you can take and apply to your own project as always im working out of rstudio ive got a script already set up here called alphacoverage.r this is basically what weve seen over the past several episodes as a starting point wev
