Published December 13, 2023
| Version v1
Publication
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Code for Micro-C data analysis and molecular dynamics simulations
Creators
Description
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
Files
Boundary_Strength.ipynb
Files
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