 I am working on my metagenomic data sets.

I have annotated my metagenome against COG database. I would like to use
DESeq to look for the overabundant genes in my site.

Here is the problem, I only have one site (one metagenome). I would like to
compare this one to different sites (each of these site has no replication
too)

the count data set looks like this:

 function name                my site      site1 (from US)    site 2 (from
Japan)  site (from Iceland) .....
COG1                                 2(counts)    6
9                         9
COG2                                 5
5                        8                          8
COG3                                 7
9                        8                             0
.....

I want to find if any of COG functions in my site is over-representative,
which means the functional gene counts are overabundant across other sites.

However, I am not sure  DESeq can do this or not?

If it can do this, how can I set the groups.

Best regards,
Ben

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