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

3.2.1 Read mapping consideration

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Last updated 6 years ago

Reads mapping consideration

In the context of Hi-C methods which are not based on restriction enzyme digestion, no filtering of restriction fragments is applied. The uniquely mapped read pairs are directly used to build the contact maps. However, during the process of ligation (with blunt ends) and sonication one may get many kinds of artifacts can be uniquely mapped to the genome, but doesn't make any sense. So we would like to dive deep into how these unwanted fragments come from.

Actually, we are more interested in intra-chromosomal interaction at 0:39.

Figure1: Summary of hic reads mapping scheme.