Two output files from summary.single

Commands in mothur
1

Hi there,

I have run the summary.single command with calc=shannon and it produced two files such as stability.opti_mcc.groups.ave-std.summary and stability.opti_mcc.groups.summary.

I can see that the values for the same sample in the two files are different. What are they? Which one should be used to get the Shannon diversity index?

Many thanks,

Dapeng

2

Hi - you should use the ave-std file. This is the result of rarefying the data. The groups.summary is without rarefaction and should not be used.

Pat

3

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