Rarefaction in mothursop

Theory behind mothur
1

Hello! I previously asked when to use the sub sampled data and sadly I am still confused. I was told “Things like amova/homova/pcoa/shannon/simpson/richness are calculated using dist.shared and summary.single using rarefaction.” and I understood that as we DO use the sub sampled data for these things.

In the mothur SOP The rarefaction step does not use the sub sampled data but to do the other alpha diversity indices in the next step, the sub sampled data IS used. I am just confused when to use the sub sampled file still.

rarefaction.single(shared=final.opti_mcc.shared, calc=sobs, freq=100) WHY NOT HERE?

summary.single(shared=final.opti_mcc.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=T) HERE

2

Hi there

Sorry for the confusion. subsampling is a single step of rarefaction. So, it wouldn’t make sense to use it in rarefaction.single() since you’d get the same result every step since the data would have already been subsampled.

I would only suggest using the subsampled shared file with things like lefse, metastats, get.communitytype.

Pat

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