question about associating count files with groups

Commands in mothur
1

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):

site 1
A 2
B 3
C 4
D 3
E 3
F 1

site 2
A 3
B 1
C 5
D 2
etc

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?)?

2

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
…

3

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.

4

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:

sequence|sample1|sample2|sample3|sample4
atttcat…|2|2|5|1

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.

5

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.

Pat