scripts used to analyse the data in the manuscript by Kaczmarczyk et al. "Search and Processing of Holliday Junctions within Long DNA by Junction-Resolving Enzymes"
System requirements:
- The analysis was performed on
- operating system MacOS High Sierra, version 10.13.6
- Python 3.9.4
The scripts are executed in Jupyter Notebook (Anaconda 4.10.1) using libraries:
- numpy 1.20.3
- matplotlib 3.4.2
- statistics
- lumicks pylake 0.10.1 (https://lumicks-pylake.readthedocs.io/en/stable/install.html#)
- scipy 1.6.3
- peakutils 1.3.3
To install the software, download Anaconda:
- Go to the Anaconda website and download the Python 3.8 (or newer) installer.
- Create a new environment for Pylake
- Install additional libraries (scipy, peakutils through Anaconda desktop app or via Terminal)
Detailed instruction on how to install Anaconda and Pylake package is available here: https://lumicks-pylake.readthedocs.io/en/latest/install.html#installation-instructions
The instalation process of Anaconda and necessary libraries requires ~15 minutes.
SCRIPTS TO ANALYSE IMAGES and FORCE (e.g. used to generate images for Figure 2) To run the scripts, put a copy of the .ipynb Jupyter Notebook in the same folder as the .H5 file you wish to analyze.
- The script will automatically load the file.
- Subsequently, it will render a kymograph and the corresponding force measurement.
- The kymograph can be then cropped and the image's brightness and contrast can be adjusted
- Within the same script, it is possible to track 1D diffusion and measure the diffusion coefficient.
OUTPUTS: -csv files with data
- png images with kymographs
- raw TIFF file
For questions, contact akaczmarczyk88@gmail.com