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. Author manuscript; available in PMC: 2023 Oct 13.
Published in final edited form as: Nat Methods. 2018 Feb 28;15(3):155–156. doi: 10.1038/nmeth.4583

Figure 1 |.

Figure 1 |

Overview of the hichipper analysis pipeline. (a) hichipper requires aligned and annotated interaction files from preprocessing tools such as Hi-C Pro2 as well as a .bed file of restriction sites. The output of hichipper can be used for quality control, visualization, and downstream topology analysis of HiChIP data. (b) Ratio of per-base coverage to local MACS-estimated local window background signal as a function of distance to nearest MboI cut site for a HiChIP sample (blue) and a ChIP-seq sample (red). Both samples represent published mouse embryonic stem cells (ESCs) with SMC1 (cohesin) ChIP1.