Analysis steps on tutorial


Sorry for too many post.
Since I checked tutorial again. I found something wired.

On analysis steps, based on tutorial…

mothur > count.groups(shared=final.opti_mcc.shared)
mothur > sub.sample(shared=final.opti_mcc.shared, size=2403)
mothur > rarefaction.single(shared=final.opti_mcc.shared, calc=sobs, freq=100)

However, when I ran sub.sample commands, it gave me the file named “final.opti_mcc.0.03.subsample.shared”

Should rarefaction.single commans like below?

mothur > rarefaction.single(shared=final.opti_mcc.0.03.subsample.shared, calc=sobs, freq=100)


Nope. rarefaction.single needs to have all the data. It effecitvely runs sub.sample 1000 times and each time it calcualtes the alpha diversity metrics and at the end reports the average and standard deviation.


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