Many observed OTU

After, data processing in step of classify.otu and then used command count.groups(shared=final.opti_mcc.shared), I got number of reads like this :

1A=90876, 2B=112856, 3C=87390, 4D=76098, 5E=89282, 6F=76401.
Then, I used command sub.sample with size = 75000. However, I got many number of observed OTUs (obs) from summary.single, showed in below:

1A=2512.91, 2B=2348.11, 3C=2833.12, 4D=2166.82, 5E=2330.93, 6F=1965.06
I’m not sure that something’s wrong or should i used subsample with other size, could you please suggest me? We used primer 341f-805R for sequencing V3V4 region.


Using V3V4 will likely generate a large number of spurious OTUs. This will be because your sequence reads do not fully overlap to adequately denoise your data. You can read this to learn more…


Thank you very much, Dr.Pat. If we can not go back to new sequencing, I should use phylotype approach.

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