Code used for the analysis of Micro-C data from the publication "In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization". Valid pair files were generated with the Micro-Capture-C pipeline. The configuration file and wrapper scripts (adapted from https://github.com/jojdavies/Micro-Capture-C/) that were used to run this pipeline are available here and can be used with the analysis scripts that are freely available for academic use on the Oxford University Innovation Software Store via https://process.innovation.ox.ac.uk/software/p/16529a/micro-capture-c-academic/1. The valid pairs file is converted into cooler format. The script can be found in: Convert_to_Cool.ipynb Visualisation of coolers are done with cooltools. The scripts for these can be found in: Plot_Matrices.ipynb Boundary_Strength.ipynb SAMD simulation was performed as described in Ohno et al (2021). Software is available at https://doi.org/10.6084/m9.figshare.13176101.v1 and is uploaded here as: HiCO_SAMD_Programs.zip HiCO SA-MD tutorial.pdf