ChIP-Seq Intensity Analysis

[solveforj]

Hello,

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.

More specifically, 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.

Thank you,

J.G.

[__sequence]

I'd say, you can calculate the coverage for all other proteins into BedGraph or BigWig files, and then intersect your BED file with the peaks of the first protein with the coverage files of other proteins, and that will give you the coverage of each of the proteins in each peak of your first protein.