rarefy guppy command

[Michael Doane]

Hey all,

I'm thinking about the idea of rarefying my samples for downstream analysis. I'm unsure how the 'rarefy' command operates in guppy. Is there a method recommended to determine what to rarefy each sample down too? I assume that best would be to determine the smallest sample then rarefy all samples to that one. However, I'm unsure how to go about determining the smallest. Do I determine the number of candidate sequences in my set of files, or am I looking for the number of placements (including pquery and multiplicities)?

Thanks in advance.

[Erick Matsen]

This is up to the user. Yes, downsampling to the smallest number of unique sequences is common.

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
http://matsen.fredhutch.org/