I am wondering how I can measure ChIP-Seq intensity at any point of an aligned genome in windows of differing length (e.g. 1023-2000 bps and 1023 to 3004 bps). I am aware of R packages like csaw, which measure intensity at bins of a predefined length, but these windows will probably overlap with the specific windows I am targeting. Any suggestions?
Update - Here is some more detail about what I am doing. I am performing a peak calling on ChIP-Seq data for 1 protein. Then, I will look at the intensities for other proteins in the same regions as the peaks for the first protein. Can I use bedtools or deeptools for this specific application?