mothur

Total Number of OTU

Commands in mothur
#1

Hi there,

I’m trying to get the total number of OTUs, so when I look at ‘stability.trim.contigs.good.unique.abund.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.tax.summary’, I found at bacteria:
total 961; O1: 223; O2:247; O3: 323; O4:265; L1:116 ; L2:262; L3:138; L4:242.

However when I look at the sobs in the ‘stability.opti_mcc.groups.ave-std.summary’,
O1:191.6; O2:194.847; O3: 323; O4:264.921; L1:113.762 ; L2:229.235; L3:124.038; L4:213.331.

So, there is a total of 961 OTUs, but the number of OTU for each samples are different in the above 2 files. Which 1 do I follow when I want to report the number of OTU for each sample?

#2

You should use the ave-std.summary file since this rarefies the data to have the same number of sequences per sample

Pat

#3

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