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
Dovetail Analysis
Topology
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Topology
Feature Discovery
AB Compartments
Topologically Associated Domains
Chromatin Loops
Comparative Analysis
Introduction
Differential Analysis