I need to know which are the OTUs that make up the unique community that I see on my venn diagram. I have been trying the ‘get.sharedseqs’ command but that doesn’t help…any ideas/suggestions?
for example, the veen reports for group 1 a total of 500 Otus unique and 800 for group 2 with only 110 shared between groups 1 and 2. How can I know which are the 500 Otus that are unique to group 1?
The confusion occurs when you have a shared file with more groups than just the 2 you are looking at in your example. For example let’s look at a simple shared file like:
Full shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
mothur > venn(groups=B-C)
Venn shared file with groups B and C selected:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
C = 0 unique OTUs
B = 2 unique OTUs
BC = 3 shared OTUs
mothur > get.sharedseqs(uniquegroups=B)
Get.sharedseqs with uniquegroups=B shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
B = 1 unique OTUs
The difference between the two commands is the groups mothur is considering when finding the unique and shared OTUs. With the venn command, mothur only uses the groups provided by the groups parameter or if none are provided the first 4 groups in the file. This is done because there are limits to the drawing of the venn diagram. With more than 4 groups the picture becomes too complicated to be of use. In this example group A is not included which changes the shared and unique composition.The get.sharedseqs command does not have the limitations of the picture. You can set parameters with the sharedgroups and uniquegroups. The sharedgroups parameter means the OTUs must include the groups you listed, but may also include other groups. The uniquegroups parameter means the OTUs must include the groups you listed and only the groups you listed.
For example:
mothur > get.sharedseqs(uniquegroups=B-C)
B-C = 0 unique OTUs (no Otus contains just sequences from B and C)
mothur > get.sharedseqs(sharedgroups=B-C)
B-C = 3 shared OTUs (3 Otus contains sequences from B and C and sequences from other groups)