Let us say I have want to use SICER or MACS2 for finding broad domains in ChIP-seq data. These contain plenty of parameters I can tune to change the domains found.
Are there any metrics I can use to see if some parameters perform better than others? Any idea, no matter how seemingly stupid, would be appreciated. If these metrics can be machine inspected so that I can automatically choose parameters that would be preferable, but any suggestions welcome.