as used by Brouwer et al.
If not done already:
Install python (at least 3.7): https://www.python.org Install pip and git First install SimpleElastix: https://simpleelastix.readthedocs.io/GettingStarted.html
Install jupyterlab and jupyter notebook
pip install jupyterlab
pip install notebook
Then install the MNase scripts (up to 5 minutes):
git clone https://github.com/Lenstralab/MNase_analysis.git
Further instructions on usage are in the ipynb file comments
Testing
This script was tested with python 3.8 on Ubuntu 20.04
Demo
For this analysis the full dataset that the script is tested on/used for is available on https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190737