Welcome to TADbit’s documentation!

TADbit is a computational package that deals with 3C-based data (more specifically Hi-C data). It handles all the steps from the alignment of paired-end reads to the detection of Topologically Associating Domain (TAD) borders, compartments and three-dimensional modeling of chromatin based on interaction matrices. The different steps:

• preprocessing of paired-end reads from Hi-C experiment

• alignment of the reads using GEM

• fitering of the mapped reads

• construction of interaction matrices and normalization

• the identification of TAD borders and compartments

• the 1D and 2D comparison of TADs

• the three-dimensional modeling of the chromatin

The library has been designed to be used by researchers with minimal level of expertise in computer science. A set of the all-in-one scripts (called TADbit tools) allow to run a full analysis in one single command line.

On the other hand, advanced users may produce their own scripts using the TADbit API.

Documentation index:

• Installing TADbit on GNU/Linux
  • Dependencies
    • Conda
    • Python libraries
    • IMP - 3D modeling
    • MCL - clustering
  • GEM Mapper
  • DryHiC for oneD normalization
  • DSRC FASTQ compressor
    • Chimera - visualization
    • LiftOver
  • TADbit
    • Conda builds
• 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
    • Comparison of Hi-C experiments
  • Three-dimentional modelling
    • Experimental data assessment and model parameters optimisation
    • Modelling a region of the chromatin
• TADbit tools
  • TADbit map
  • TADbit parse
  • TADbit filter
  • TADbit normalize
  • TADbit bin
  • TADbit segment
  • TADbit model
  • TADbit merge
  • TADbit describe
  • TADbit clean
  • TADbit import
  • TADbit export
• Reference Guide
  • From FASTQ to matrix
    • Mapping
    • Quality check and plotting
    • Filtering
  • Chromosome class
    • Load chromosome
    • ExperimentList class
  • Experiment class
    • Load experiment
  • HiC_data class
  • TAD detection functions
  • TAD clustering
  • Parsers
  • Boundary Aligner
  • Alignment class
  • IMPoptimizer class
  • IMPmodel class
  • StructuralModels class
  • Utilities
• Bibliography