I am not sure what tool you are using, but once peaks are called the output can be filtered/compared to determine those with the most coverage/depth. See the tools in the group NGS: Peak Calling at Galaxy Main (http://usegalaxy.org) if you have not chosen one yet. Review the tool forms and 3rd party documentation to understand the output metrics and what they represent.
If you are looking for a tutorial and/or examples for how to perform the analysis, googling "galaxy chip-seq" brings up many learning options.
Thanks, Jen, Galaxy team