Analysis of HiChIP Data.

HiChIP is a novel method for the analysis of chromatin interactions based on in situ Hi-C that adds an immuno-precipitation (ChIP) step for the investigation of chromatin structures driven by specific proteins. This approach has been shown to be very efficient as it reliably reproduces Hi-C results and displays a higher rate of informative reads with a required lower amount of input cells when compared with other ChIP-based techniques (as ChIA-PET). Although HiChIP data preprocessing can be performed with the same methods developed for other Hi-C techniques, the identification of chromatin interactions needs to take into account specific biases introduced by the ChIP step. In this chapter we describe a computational pipeline for the analysis of HiChIP data obtained with the immuno-precipitation of Rad21 (part of the cohesin complex) in human embryonic stem cells before and after heat-shock treatment. We provide a detailed description of the preprocessing of raw data, the identification of chromatin interactions, the evaluation of the alterations induced by treatment, and, finally, the visualization of differential loops.