PEAK-A-VIEW ( •̀ ω •́ )✧

Project Description

CSE 185 Final Project: Peak Calling Implementation for Mouse Liver ChIP-seq

Title/Description: PEAK-A-VIEW

peak-a-view is designed to process ChIP-Seq data to identify peaks corresponding to key regions representing protein-DNA interactions.

Table of Contents

• Contributions
• Installation
  • Setting Up the Environment
• Usage
  • Basic Usage Instructions
  • Complete Usage Instructions
• Project Structure

Contributions

• Jiyeon Song: jis036@ucsd.edu
• Ivana Roque: iroque@ucsd.edu
• Jacob Ketchum: dketchum@ucsd.edu

Installation

Setting Up the Environment

1. Clone the repository:

   git clone https://github.com/jiyeonsongg/peak-a-view.git
   cd peak-a-view

2. Set up the requirements:

   pip install -r requirements.txt

3. Install peak_a_view.py:

   python setup.py install

4. Verify the installation:

   which peak_a_view  # or `where peak_a_view` on Windows

5. Get started!

   peak_a_view --help

   EXAMPLE:

   peak_a_view small_ENCFF609LFX.bam -o output_peaks.bed -w 500
   # peak_a_view INPUT.bam -o OUTPUT.bed -w WINDOW_SIZE_NUMBER

Usage

Basic Usage Instructions

A peak calling tool using a Python script and visualization methods. Compare with the peak calling algorithm findPeaks.

Complete Usage Instructions

Once we export the output_peaks.bed after running the command line, open IGV(Integrative Genomics Viewer) and upload the file to see peak calling visualization.   Recommendation: Download IGV Desktop version - https://igv.org/

Project Structure

peak-a-view
|
|--analysis
|--benchmark
|--peak_a_view
|  |  __init__.py
|  |  peak_a_view.py
|  |  peak_a_view_tool.py
|  |  test_peak_a_view.py
|--tests
|  |  cmdline_tests.sh
|--.gitignore
|--README.md
|--requirements.txt
|--setup.py

Testing

To run unit tests:

• Ensure you are in peak-a-view/peak_a_view directory
• Run: python test_peak_a_view.py

To run command line tests:

• Run chmod +x cmdline_tests.sh from inside the peak-a-view/tests directory
• Ensure you are in peak-a-view/tests directory
• Run command ./cmdline_tests.sh