Tutorials

From FASTQ files to interaction matrices

• Retrieve HiC dataset from NCBI
• Preparation of the reference genome
• Hi-C quality check
• Iterative vs fragment-based mapping
• Mapping
• Load mapped read-ends and generate a matrix
• Quality check of the Hi-C experiment
• Filtering
• Bin filtering and normalization

Identification and Analysis of TADs and Compartments

• Compartments and TADs detection
  • Compartments
  • TADs
  • Comparison of TAD borders
• Comparison of Hi-C experiments
  • Comparison between replicates
  • Comparison between cell types
  • Merge Hi-C experiments
  • Normalizing merged data

Three-dimentional modelling

• Experimental data assessment and model parameters optimisation
  • Data preparation
  • Data modellability assessment via MMP score
  • Data Transformation and scoring function
• Modelling a region of the chromatin
  • Load previous data
  • Modeling
  • Structural Models
  • Align models
  • Deconvolve
  • Clustering
  • Consistency
  • DNA density plots
  • Walking Angle
  • Particles interactions
  • Accessibility
  • Calculating distances between particles