venn

Commands in mothur
1

I was having 4370 OTUs from 25 samples. I had to make two groups of samples, and divided 25 samples in two groups in design file (high and low fic groups).
I wanted to present venn diagram between these groups. I merged the samples using merge.groups command, then run the venn command on output shared file.

mothur >
merge.groups(shared=stability.an.0.03.subsample.shared,design=lakes.10fic.design)
0.03

Output File Names:
stability.an.0.03.subsample.merge.shared

mothur >
venn(shared=stability.an.0.03.subsample.merge.shared)
0.03

Output File Names:
stability.an.0.03.subsample.merge.0.03.sharedsobs.High_FIC-Low_FIC.svg
stability.an.0.03.subsample.merge.0.03.sharedsobs.High_FIC-Low_FIC.sharedotus

However, the output figure displays only 1232 OTUs in total and 304 shared OTUs.
Please point out my mistake and suggest me how get all OTUs in the figure?

2

I wonder whether you looked in the third column of summary.shared on stability.an.0.03.subsample.shared or if you saw that it has an OTU named OTU4370. When you subsample, you have some OTUs drop out and I would believe the number of total OTUs woudl drop once you subsample.

Pat

3

I summed the number of Sobs of all samples. Does it not indicate number of OTUs?

4

If some of the OTUs are shared between samples then your sum of richness values would be more than the actual number of OTUs across all samples. Maybe I’m missing something. If so, could you post some specifics?