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:

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: