I made a venn diagram to look at the total number of observed OTUs between my samples, but now I was wondering if and how can I know which OTUs (sequences) are being shared between the samples. Is there a command I can write to show me which are the OTUs shared in the construction of the venn diagram?
The command you are looking for is get.sharedseqs, http://www.mothur.org/wiki/Get.sharedotu. You must provide a list and group file. Pay close attention to the difference between entering your groups under the unique or shared parameter. If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups. If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups. If you set unique=A-B, and an otu contains sequences from groups A, B and C, it will not be included in the output, but shared=A-B would include it. I hope this helps.