How to generate BED files with 3D coordinates?

Question

[jetson]

I'm analyzing some HiC data for the 1st time. I need to generate a 3D model of the data. For visualization, I require the format to be in .pdb or .g3d (as described in https://g3d.readthedocs.io/en/latest/g3dtools.html). I have been going through a lot of literature related to the methods for 3D models (MDS, probability based methods etc) but I can't find straightforward documentation for generating the files. Could I please get some directions? Thanks.

Answer 1

[xubeisi]

you need model the Hi-C contact matrix to 3d coordinate first, then convert to g3d format, below sum available tools

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

[jetson]

Thanks @xubeisi. I will check it out.