3dgenome
  • Initial page
  • Cover
  • Preface
  • Figurelist
  • Chap0 Preparation
    • 0.1 Molecular biology
    • 0.2 Sequencing technologies
    • 0.3 RNA-seq Data Mapping & Gene Quantification
    • 0.4 RNA-seq Differential Analysis
  • Chap1 Why we care about 3D genome
    • 1.1 From 2D to 3D nuclear structure
    • 1.2 From static to dynamic
    • 1.3 From intra to inter chromosomes "talk"
    • 1.4 From aggregation to division - phase separation
  • Chap2 experiment tools for exploring genome interaction
    • 2.1 Image based
    • 2.2 Primary order
    • 2.3 Higher order C-techs
  • Chap3 Computational analysis
    • 3.1 Primary order analysis
    • 3.2 Higer order data analysis
      • 3.2.1 Read mapping consideration
      • 3.2.2 Analytical Pipelines
        • GITAR Pipeline
        • HiC-Pro Pipeline
      • 3.2.3 TAD calling algorithms
    • 3.3 3D structure
  • Chap4 RNA-genome interaction
    • 4.1 Experimental Methods
    • 4.2 Computational Analysis
  • Chap5 Integrative Data Visualization Tools
    • 5.1 GIVE
    • 5.2 HiGlass
  • Chap6 4DN Project
  • Appendix
    • Homework
    • Student's presentation
      • A Brief Introduction to Machine Learning
      • Precision medicine
      • CHIP-Seq
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  1. Chap3 Computational analysis
  2. 3.2 Higer order data analysis

3.2.2 Analytical Pipelines

With feature-rich Hi-C analysis, from Raw data download and pre-processing, to visualization and understanding the topological relationship, comprehensive and user-friendly tools (various feature extraction may need many dependencies which could be annoying installation) are wanted. Although some tools are specialized in specific problem, others that integrate the whole pipeline will be introduced here.

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Last updated 6 years ago