Hi all! Ive done the Mothur MiSeq sop a million times now for my masters thesis and I am still a little unsure what the use of the output from sub.sample is? We use the output for Make.shared for Alpha and beta diversity and Ive used it for relative abundance analysis as well. Ive never used the sub sampled data. Why do it, if we never use the files it creates? Am I missing something?
Im still new to normalization and sub sampling and what the utility is so I could just be generally confused.
Any clarification would be so helpful.
The output for sub.sample would be used for things like metastats/lefse/machine learning - anything where you need relative abunance data calculated on the same number of sequences per sample. Things like amova/homova/pcoa/shannon/simpson/richness are calculated using dist.shared and summary.single using rarefaction.