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README.md

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Repository Overview

This repository contains scripts and tools for analyzing nucleosome positions in cfDNA sequencing data, simulating nucleosome configurations, and performing downstream analyses.

System Dependencies

In addition to the Python packages listed in requirements.txt, the following system dependencies are required to run the scripts:

  • GNU Parallel: Install using your package manager. For example:

    • On Ubuntu: 
      sudo apt-get install parallel
    • On macOS: 
      brew install parallel

  • samtools: A suite of programs for interacting with high-throughput sequencing data. Install using your package manager:

    • On Ubuntu: 
      sudo apt-get install samtools
    • On macOS: 
      brew install samtools

Make sure to install these dependencies before running the scripts.

Additional Information

For more detailed information about specific scripts and analyses, please refer to the README files located in the different folders of the repository.