Well, it would help if we had a few more details, but to calculate the
number of reads within each 1kb window of the genome, it's something like:

library(BSgenome.Hsapiens.UCSC.hg18) # assuming human
widths <- rep(1000, seqlengths(Hsapiens)[1]/1000)
# assuming 'cov' is a coverage Rle for chr1
windows <- successiveViews(cov, widths)
x <- viewSums(windows)/1000

That should get you the numbers you need for that scatterplot.

Michael

On Tue, Aug 25, 2009 at 7:11 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:

> Hi everyone,
>
> please could you let me know if there is any way to represent in a 2D plot
> the number of ChIP-seq tags / 1kb genome window for 2 experiments ? eg :
>
> on X axis : the number of tags / 1kb window  for protein 1;
> on Y axis : the number of tags / 1kb window for protein 2;
>
> thanks very much.
>
> -- bogdan
>
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