let’s say I have 3 treatment sites
and my data has been tabulated as follows, in count files (a-f being the taxa, the numbers being the counts at various sites):
when i want to do community analysis after alignment of A-F sequences, how do I associate these different count files with different groups (how do I separate them as different treatments?)?
I think what you are looking to do is make something like mothur’s count table, http://www.mothur.org/wiki/Count_File.
Representative_Sequence total site1 site2
A 5 2 3
B 4 3 1
C 9 4 5
D 5 3 2
How do you incorporate that into analysis; venn, parsimony, rarefaction, etc?
Do you still need group files if you have the count file (it has the groups already listed at the top).
I’m at the cluster phylip step of SOP, I see there’s a count function in that module…once I incorporate it here, do I need it for further use?
thanks for the help as always.
Sorry to flood the board
let me start from the beginning.
I have 4 sampling points, and the way my data is given to me is as such:
as opposed to a raw list of sequences (basically a count file). this, so far, has proven incredibly difficult to work with, and I’m not really sure where to start (with the ultimate goal of PCA, rarefaction, and other inter-sample comparisons). Any help formatting this properly would be helpful. Should I start a new topic on this? I’m lost.
I would suggest transforming your table into a count table. Where are you getting the data in this format from? You’ll likely have to write a script or do some R/Excel magic to convert it to a count table.