In the control samples, we often observe tag distributions with local fluctuations and biases. For example, at the FoxA1 candidate peak locations, tag counts are well correlated between ChIP and control samples (Figure 1c,d). Many possible sources for these biases include local chromatin structure, DNA amplification and sequencing bias, and genome copy number variation. Therefore, instead of using a uniform λBG estimated from the whole genome, MACS uses a dynamic parameter, λlocal, defined for each candidate peak as:
