Promoters and enhancers are two categories of well-understood regulatory regions. There exist many other types of genomic regions also bound by DNA proteins. For example, cohesion proteins CTCF and RAD21 usually bind at the boundaries of topological associated domains and play a key role in the 3D chromatin structure [19]. Transcription initiation protein POLA2 binds to all active regulatory regions in the whole genome. For such proteins, it is important to call their ChIP-seq peaks from the whole genome, using the ‘-WG’ mode of ChIP-BIT2. As no annotated regulatory regions were needed, ChIP-BIT2 modeled read intensities from sample and input ChIP-seq profiles and predicted peaks at genome-wide locations.

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