4D Genome Browser Documentation

The 4D Genome Browser

• Getting Started

The 4DGB Workflow Tool

• Getting Started (v1.5.6)
• Installing the 4DGBWorkflow tool
• Running an example project
• Getting started with your own data
  • Progressively Adding Information
• The Project.yaml file
  • Workflow section
  • Project section
  • Datasets Section
  • Tracks Section
  • Bookmarks section
  • Annotations section
• File formats
  • Track data (.csv)
  • Features file (.csv)
• Copying and sharing an existing project
  • Sharing Results
• Working on Windows OS

File Conversion and Preprocessing

• Hi-C File Converter
  • Installation and setup
  • Dependencies
  • Example usage
  • A Note on size file
• Activate and inactive X
  • Generating a .hic file from a .summary.txt.gz
• Hi-C data of embryonic stem cells
  • File gathering and preprocessing
  • Restriction sites
  • Paired-end alignment
  • Hi-C analysis
• A549 Cells
  • File gathering and preprocessing
  • Restriction site marking and indexing
  • Building a contact map for chromosome 22
  • Converting the .h5 contact map to .hic
• Useful commands for 4DGB project
  • Generating a .hic file.
  • Formatting with Juicer Pre
• Work Cited