This repository contains python scripts and parameters for reproducing the simulations described in our work using Optical Reconstruction of Chromatin Architecture to in mouse embryonic stem cells, with and without cohesin and CTCF. The simulation code is contained in the python script, PolymerSims.py. Example parameters for simulations with and without cohesin are included in the ADsimPars.txt and NTsimPars.txt. Parameters used in other simulations are described in the Methods of our paper.
To run, this code requires the polychrom repository, available at https://github.com/open2c/polychrom To ensure compatability, we recommend using these simulations with our lab's fork of the polychrom project, available at https://github.com/BoettigerLab/polychrom