I am using mothur for my 16S rRNA data. I have several groups I want to compare statistically, however, the “mouse.time.design” in MiSeq SOP only compare two groups (Early vs. Late). I have tried to add more groups, but it does not work. It must be possible to add more than 2 groups in the design.file? It would be very helpful to see an example of a design.file in which several groups are included.
Thank you very much!
You would change the “Early” and “Late” to the names of the groups you are interested in. Can you post your design file and the error you are getting?
Great, thank you! It works fine when the groups are the same in both of these files “design.file” and “stability.an.thetayc.0.03.lt.ave.tre”. However, if I only want to include a subset of the groups from the file “stability.an.thtay…”, should I choose another size here: mothur > sub.sample(shared=stability.an.shared, size=2241), or should I make another “stability.file” and run all the steps from the beginning?
It is perhaps a way of specifying the groups to be used from the file “stability.an…” when I use this command:
parsimony(tree=stability.an.thetayc.0.03.lt.ave.tre, group=mouse.time.design, groups=all)? I tried to specify the groups in groups=cDNA10-cDNA11-cDNA12-cDNA13, but this does not work.
my design file is shown here:
The groups parameter in the parsimony command is used to select items from the second column of the group or design file. If you would like to select of remove groups from your files you can uses the get.groups and remove.groups commands. http://www.mothur.org/wiki/Get.groups http://www.mothur.org/wiki/Remove.groups
Great, that was very helpful, thank you very much