Dovetail Analysis

Data Processing

  • Before you begin
  • Pre-Alignment
  • From fastq to final valid pairs bam file
    • Alignment
    • Recording valid ligation events
    • Sorting the pairsam file
    • Removing PCR duplicates
    • Generate .pairs and bam files
    • Generating the final bam file
  • Generating Contact Matrix
    • Generating HiC contact maps using Juicer tools
      • Additional Dependencies
      • From .pairs to .hic contact matrix
      • Visualizing .hic contact matrix
    • Generating cooler contact maps
      • Additional Dependencies
      • From .pairs to cooler contact matrix
      • Genereting multi-resolutions files and visualizing the contact matrix

Whole Genome Sequencing

  • Quality Control & Sequencing Requirements
    • Complexity
    • QC Assessment
    • Sequencing Recommendations
  • Detection of Genetic Variants
    • Structural Variants
    • Copy Number Variation
    • SNVs and Indels
  • Topology
    • Feature Discovery
      • AB Compartments
      • Topologically Associated Domains
      • Chromatin Loops
    • Comparative Analysis
      • Introduction
      • Differential Analysis
  • Comparative Analysis
    • Introduction
    • Differential Analysis
  • Phasing
    • Compatible Tools
  • Genome Assembly
    • Compatible Tools
  • Datasets

HiChIP

  • Quality Control & Sequencing Requirements
    • Proximity-ligation assessment
    • ChiP enrichment
      • Calculating enrichment stats
      • Plotting global enrichment around ChiP peaks
    • QC Assessment
      • Pass/No Pass Metrics
      • Pass/No Pass Values
      • Visual Inspection Of The Alignments
      • Final Determination
  • Loop Calling
    • Introduction
    • Resolution
    • Tool landscape
    • Why FitHiChIP?
    • Input files
    • Tools
    • Workflow Overview
    • Output
    • What if?
    • What next?
  • HiChIP Comparative Analyses
    • Introduction
    • Differential Analysis
  • Plotting HiChIP Data
    • Introduction
    • Inputs
    • Tools and Data Used
    • Basic Workflow
    • Walkthrough
      • There’re figures, then there are Figures
  • Calling 1D peaks with MACS2 on HiChIP data
    • Introduction
    • Input files
    • Additional tools needed
    • Workflow Overview
    • Workflow
  • Datasets

Capture

  • Quality Control & Sequencing Requirements
    • Proximity ligation properties
    • Target enrichment QC
      • On-target rate
      • Coverage depth
    • Replica Reproducibility
  • Detection of DNA Looping Interactions
    • Introduction
    • Input files
      • Genomic fragments and design directory
      • chinputs
    • Interaction calling
    • Output files
      • Diagnostic plots directory (diag_plots)
      • Examples directory (examples)
      • Data directory (data)
      • Optional - Enrichment plots directory (enrichment_plots)
    • Additional suggestions for interactions data analysis:
    • For advanced users
      • Generate your own CHiCAGO design directory
  • Capture Comparative Analysis
    • Introduction
    • Input files
      • Peak files
      • Design Library
      • Chinputs
    • Calling differential interactions
  • Datasets
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