Plotting MeDIP-seq vs genes of interest

[AmyK]

I have MeDIP-seq reads for each chromosome and the resolution is 100 bp. My questions is how can I plot read counts vs genes of interests. From USCS browser, I can get location of these genes and their coordinate on the chromosome.
Take for example data on chr1 looks like this:
0 20 0 0 35 0 0 ....
data is recorded after each 100 base pair. But I dont know how to map my read counts to chromosome coordinates. I'm also using matlab.
I'm new to this field and any help or suggestion will be greatly appreciated !
Amy-

[nilshomer]

Please make sure that you don't post the same question in two forums.