Hi folks, i wonder what is the best way to figure the number of OTU and sequences that are unique to a given group i.e. not shared with any other groups?
here is what i did:
i used the get.sharedseqs command with the uniquegroup=a group option. it returned what i believe the OTU number, but not the sequences.
any help is appreciated
If you provide the fasta file mothur will output the sequences unique to that group. http://www.mothur.org/wiki/Get.sharedseqs#fasta
thanks you. I was a bit lost in the terminology. Ideally, there is no such a thing as “shared” sequences. Simply because each sequence comes from one sample only. However, there is shared unique sequences or shared OTU (at 0, 3%, etc). And the shared sequnces are the sequcnes represented by whatever OTUs…
Again, this just means that 2 OTUs can be shared between 2 samples without sharing any sequences or unique sequences.
… the command get.sharedseqs is a bit confusing as it, on the screen, returns the number of shared OTUs.
now, that was the process of my thinking. The conclusion that reached is that shared sequeces (or rather sequences representing shared OTUs) don’t really mean anything or has any benefit over the shared OTU.
I ended up computing only shared otus using summary.shared. I Also used get.sharedseqs with uniquegroup option to get the non-shared otus (sample exclusive)
very extra notes:
-the use of unique as meaning non shared is confusing here as unique means a similarity close to 0
- the name of the command get.sharedseqs is a bit confusing as it, on the screen, returns the number of shared OTUs.
-using the calculator sharednseqs with summary.shared for two samples, returns the sum of those sequences.
hope this feedback be helful