A signal-noise model for significance analysis of ChIP-seq with negative control.

Xu H,    Handoko L,   Wei X,   Ye C,    Sheng J,    Wei CL,    Lin F,   Sung WK.

CCAT (Control-based ChIP-seq Analysis Tool) implements a signal-noise model to identify significant ChIP-seq peaks or regions, by comparing a ChIP library and a control library.

Program availability : CCAT3.0.tar.gz

The original paper can be found in here.