Promoters refer to the proximal regulatory regions centered around gene TSS. A TSS annotation file is required to enable the ‘-promoter’ running mode of ChIP-BIT2. Users can set the preferred promoter size using the ‘-s’ option. Under this mode, ChIP-BIT2 jointly modeled read intensities in the sample and input ChIP-seq profiles using the Gaussian mixture model [Eq. (2)]. In the meanwhile, it modeled the relative distance of each window to the nearest TSS using the Exponential-Uniform mixture model [Eq. (3)]. A demo of using ChIP-BIT2 for detecting peaks at promoters was provided in Additional file 1: Fig. S4.

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