Opti_mcc file confusion

Theory behind mothur
1

Hi all! I am trying to understand all my outputs from mothur so I can understand which microbes are most abundant in my samples. Is this understanding below of these two files correct? The definition of size is in the Miseq SOP but I was a little confused about “total”

  • (final.opti_mcc.shared) total = how many sequences are in that otu
  • (final.opti_mcc.0.03.cons) Size = How many times the Otu was observed in the sample and it also has the consensus taxonomy from our different sequences
2

Hi there,

Hmmm. I’m not sure what you mean by a “total” column in a shared file. That file should have the label (i.e. the OTU definition), the group or sample name, the numOTUs (number of OTUs observed across all samples), and then separate columns for each OTU. Those columns will have the number of times each OTU was seen in each sample. Let me know if you’re looking at a different file. Perhaps you aren’t including the full filename extension?

For *.cons, I think you mean *.cons.taxonomy… The Size column is the number of times that OTU was observed across all of the samples.

Pat

3

I think I had created a column labeled “total” with the number of OTUs observed across all samples columns in the shared file actually :downcast_face_with_sweat:.

From what you said, it seems like the numbers in each OTU column in the shared fileareadded up for the Size column in the .cons.taxonomy file.

Is this understanding correct?

4

Yep, I think you’ve got it

5

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