This repository contains the code and data needed to generate the figures for the following manuscript:
3D chromatin interactions involving Drosophila insulators are infrequent and arise before TADs and transcription
Olivier Messina [1], Flavien Raynal [2], Julian Gurgo [1], Jean-Bernard Fiche [1], Vera Pancaldi [2,3], Marcelo Nollmann [1]
[1] Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, Montpellier, France. [2] Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France. [3] Barcelona Supercomputing Center, Barcelona, Spain.
The repository contains the following scripts:
- HiC_Aggregation_Analysis.m
This is a Matlab script used to compute Aggregation Peak Analysis for chromatin binding factors. The functions used in this script are encoded in an additional file called functionsContainer.m
- HiM_matrices_plots.m
This is a Matlab script used to compute pair-wise distance and proximity maps.
- HiC_ChAs_Analysis.R
This is a R script used to compute ChAs analysis for chromatin binding factors.
The latest version of the data can be found at: https://osf.io/aqtxj/.
You will be able to download a Numpy array with the pair-wise distance maps for each of the datasets available:
- Drosophila melanogaster, dpp locus, nuclear cycle 12
- Drosophila melanogaster, dpp locus, nuclear cycle 14