This repository contains the scripts used to produce the simulations presented in the preprint by (Ya et al., 2022). The simulations are based on the polychrom software (Version v0.1.0, 10.5281/zenodo.3579473, Imakaev et al., 2019), and scripts were adapted for our purposes from the open source code of polychrom, and their loop extrusion example found at https://github.com/open2c/polychrom.

Information on how to run the simulations are included in every subdirectory with the different cases, under runs.txt

Simulations are run on a NVIDIA GPU-equipped workstation, and minor adjustments will be needed for computation on non-cuda machines.