We provide IPython Notebooks (in jupyterNotebooks) containing all the steps from the obtention of the interest interaction matrices from BAM files, to their normalisation, modelling, and further analysis. As it was done in:
3D reconstruction of genomic regions from sparse interaction data.
Julen Mendieta-Esteban, Marco Di Stefano, David Castillo, Irene Farabella, and Marc A Marti-Renom.
https://www.biorxiv.org/content/10.1101/2020.10.11.334847v1.full.pdf
Intermediate files and additional information are also included.
To start using this Git, go to jupyterNotebooks folder and run the notebooks inside of the folders in numeric order