Kaczmarczyk-et-al.-Search-and-Processing-of-Holliday-Junctions-

<p><strong>Kaczmarczyk-et-al.-Search-and-Processing-of-Holliday-Junctions-</strong></p> <p>scripts and the raw data used&nbsp; in the manuscript by Kaczmarczyk et al. &quot;Search and Processing of Holliday Junctions within Long DNA by Junction-Resolving Enzymes&quot;</p> <p>System requirements:</p> <ul> <li>The analysis was performed on</li> <li>operating system MacOS High Sierra, version 10.13.6</li> <li>Python 3.9.4</li> </ul> <p>The scripts are executed in Jupyter Notebook (Anaconda 4.10.1) using libraries:</p> <ul> <li>numpy 1.20.3</li> <li>matplotlib 3.4.2</li> <li>statistics</li> <li>lumicks pylake 0.10.1 (<a href="https://lumicks-pylake.readthedocs.io/en/stable/install.html#">https://lumicks-pylake.readthedocs.io/en/stable/install.html#</a>)</li> <li>scipy 1.6.3</li> <li>peakutils 1.3.3</li> </ul> <p>To install the software, download Anaconda:</p> <ol> <li>Go to the Anaconda website and download the Python 3.8 (or newer) installer.</li> <li>Create a new environment for Pylake</li> <li>Install additional libraries (scipy, peakutils through Anaconda desktop app or via Terminal)</li> </ol> <p>Detailed instruction on how to install Anaconda and Pylake package is available here: <a href="https://lumicks-pylake.readthedocs.io/en/latest/install.html#installation-instructions">https://lumicks-pylake.readthedocs.io/en/latest/install.html#installation-instructions</a></p> <p>The instalation process of Anaconda and necessary libraries requires ~15 minutes.</p> <p>&nbsp;</p> <p>To run the scripts, put a copy of the .ipynb Jupyter Notebook in the same folder as the .H5 file you wish to analyze.</p> <p>&nbsp;</p> <ol> <li>The script will automatically load the file.</li> <li>Subsequently, it will render a kymograph and the corresponding force measurement.</li> <li>The kymograph can be then cropped and the image&#39;s brightness and contrast can be adjusted</li> <li>Within the same script, it is possible to track 1D diffusion and measure the diffusion coefficient.</li> </ol> <p>OUTPUTS: -csv files with data</p> <ul> <li>png images with kymographs</li> <li>raw TIFF file</li> </ul> <p>For questions, contact <a href="mailto:akaczmarczyk88@gmail.com">akaczmarczyk88@gmail.com</a></p>