Welcome to FitHiChIP!

Developers: Sourya Bhattacharyya, Ferhat Ay

Institution: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA

Utilities of FitHiChIP at a glance

• FitHiChIP derives the statistically significant CIS interactions from a given HiChIP / PLAC-seq, and now for Hi-C data as well.

  • CIS Interactions within a specified distance range (default = 20 Kb to 2 Mb: can be user defined) and for a specified fixed size bin size, are computed.

  • Distance decay model proposed in the method FitHiC (Ay and Noble, Genome Research 2014) together with a novel bias (coverage / ICE) regression model is used to find the statistical significant interactions.

• Processing HiChIP / PLAC-seq requires specifying ChIP-seq peaks corresponding to the target protein or histone modifications of interest.

  • Either user can provide ChIP-seq peak files from ENCODE, ROADMAP, or any other reference.

  • Alternatively, FitHiChIP supports calling peaks from HiChIP data, which can be used to find out the interactions involving peaks (enriched) segments.

• FitHiChIP also supports finding differential HiChIP contacts between two different categories of HiChIP data, having one or more replicates.

• FitHiChIP also proposes a basic implementation of simulating HiChIP contact map given a reference HiC contact map and a ChIP-seq alignment file, with respect to specified number of reads. (Note: this implementation is still in basic stage; output HiChIP heatmap shows explicit bias towards low range contacts.)

Repository

FitHiChIP is hosted in https://github.com/ay-lab/FitHiChIP

Execution

Details of execution commands and parameters are provided in the below mentioned links:

• Installation
  • Option 1: Install from source in GitHub
  • Option 2: Running FitHiChIP with Docker or Singularity
• Quick start
  • Description of the test data
  • Configuration parameters according to the test data
  • Sample logs from the console, corresponding to the TestData
  • Output file description
• Setting up configuration file
  • Input HiChIP contact matrix file - different formats supported
  • Other files / directories
  • Execution options
• Details of FitHiChIP outputs
  • Summary HTML file
  • Details of output files
  • Details of FitHiChIP significant interactions
  • Details of merge filtering output
  • Visualizing significant interactions in epigenome browsers
  • Visualizing significant interactions (after merge filtering) in epigenome browsers
• Differential analysis of HiChIP loops
  • Basics
  • Options
  • Example 1
  • Example 2
  • Details of differential analysis outputs
• Various utility scripts / functions
  • 1. generating contact matrices of different resolution (bin size)
  • 2. inferring peaks from HiChIP data (for use in the HiChIP pipeline)
  • 3. merging a set of ChIP-seq alignment files
  • 4. Producing FitHiChIP loops with different FDR thresholds
  • 5. Applying merge filtering on any set of significant loops (generated by FitHiChIP or any other loop calling method)
  • 6. Visualization of the significant loops in WashU epigenome browser
  • 7. Simulating HiChIP contact matrix from HiC and ChIP-seq data
  • 8. Applying FitHiChIP on capture HiC data
• Frequently asked question
  • How do I cite FitHiChIP?
  • I do not know anything about HiChIP. What should I do?
  • How to install HiC-pro in the system?
  • How to visualize the FitHiChIP loops in genome browser?
  • What type of input data formats are supported in FitHiChIP?
  • What type of HiChIP interactions are supported in FitHiChIP?
  • Does FitHiChIP support processing HiC data?
  • I want to process HiChIP data, but cannot find any reference ChIP-seq file. What should I do?
  • Does FitHiChIP support processing Capture-HiC data?

Citation

FitHiChIP is now published at Nature Communications (<https://www.nature.com/articles/s41467-019-11950-y>)

If you are using FitHiChIP, please cite:

Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, and Ferhat Ay, Identification of significant chromatin contacts from HiChIP data by FitHiChIP, Nature Communications, Vol 10, No 4221, 2019, DOI: <https://doi.org/10.1038/s41467-019-11950-y>

Support

For any queries or problems, user can report an issue in GitHub (<https://github.com/ay-lab/FitHiChIP>). Alternatively, user can mail us in:

• Sourya Bhattacharyya <sourya@lji.org>

• Ferhat Ay <ferhatay@lji.org>