README.txt

This directory contains the data and scripts required to generate the plots and analysis in the paper:

Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells
Elsie C. Jacobson,  Jo K. Perry, David S. Long, Ada L. Olins, Donald E. Olins, Bryon E. Wright, Mark H. Vickers, Justin M. O'Sullivan
https://www.biorxiv.org/content/early/2018/06/05/339085

The 00_RNAseq folder contains the featureCounts matrix and all downstream gene expression analysis
The 01_Hi-C folder contains scripts that require DGE data, so it is recommended that the RNAseq scripts are run first

The folders are structured:
/data contains pre-processed data required for the analyses
/scripts contains the scripts
/results contains all non-plot outputs of the scripts
/plots contains the plots generated by the scripts
README.txt contains more specific details for the folders

Raw interaction data is too large to track in GitHub, therefore you need to get the 6 files from figshare (https://figshare.com/s/1f6f85129a647ac2f3f7) and add them into the 01_Hi-C/data/ directory.