3DChrom: Reconstructing three-dimensional structures of chromatins and TADs using Hi-C data and MDS methods

Help Page


Given a symmetric Hi-C contact matrix, 3DChrom can reconstruct three-dimensional (3D) structures of chromatins or topologically associating domains (TADs). The methods are described as follows:


  1. Converting Hi-C contacts into wish distances. We define two mutually exclusive Hi-C contact sets based on whether Hi-C contacts equal zero: C1 and C2. The wish spatial distancs are obtained from the equaltion distance, where α is set to 1/3 and β is the scale parameter (default 1).

  2. Defining objective functions to get the optimal coordinates in 3D space in accordance with the wish distancs. Here we provide three objective functions.

    • PASTIS from PASTIS.

    • ChromSDE from ChromSDE.

    • self-defined self-defined with R equal to maximum wish distance or using shortest path to infer the with distance of missing Hi-C contact.

  3. Obtaining optimal solutions (i.e., 3D coordinates) for the three objective functions using IPOPT.