How would be the easiest way to get the otu nr.s for three groups venn style. Otus that are unique per group, shared by all, shared by any pairwise comaprision.
I get that I could wrang it out from a share-d file by messing with spreadsheets or scripting, but are there any commands in mothur that would do it?
I get that by Get.otu command I could get a sum of otu-s in two groups, but are there possibility to get otus that are unique to one or another or those that are shared.
Ok it seems that get.sharedseqs might do the trick? THough it lists sequences, it will also have Otu nr available in the output. Cant there be an output of just otus also? Looks that I have to do some scripting or spreadsheet work nonetheless?
I still want to clarifify as I do not understand the wiki completely.
The shared and unique options.
I have groups A,B and C.
Lets say I want otus shared between A and B, but NOT with C. Should I then put in get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, unique=A-B), or willl it just give two sets otus unique to A and then otus unique to B.
Command get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, shared=A-B) should give me the ones shared by all.
And at the single ones I can put.
get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, unique=A)
get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, unique=B)
get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, unique=C)
So I only have a doubt with the pairwise comparisions, otherwise I can get the “venn diagram” information I guess.
In version 1.29.0, the venn command creates a *.sharedotus file that includes the labels of the otus represented by each piece of the venn diagram. You can also use the get.sharedseqs command.
Lets look at an example: http://www.mothur.org/wiki/Example
To get the sequences in the 23 OTUs unique to A: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=A)
To get the sequences in the 21 OTUs unique to B: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=B)
To get the sequences in the 15 OTUs unique to C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=C)
To get the sequences in the 15 OTUs shared by A + B: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, shared=A-B)
To get the sequences in the 8 OTUs shared by A + C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, shared=A-C)
To get the sequences in the 6 OTUs shared by B + C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, shared=B-C)
To get the sequences in the 11 OTUs unique by A + B: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=A-B)
To get the sequences in the 4 OTUs unique by A + C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=A-C)
To get the sequences in the 2 OTUs shared by B + C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=B-C)
To get the sequences in the 4 OTUs unique by A + B + C: get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, unique=A-B-C)