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.)
Details of execution commands and parameters are provided in the below mentioned links:
- Quick start
- Setting up configuration file
- Details of FitHiChIP outputs
- Differential analysis of HiChIP loops
- 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 HiChIP interactions are supported in FitHiChIP?
- Does FitHiChIP supports processing HiC data?
- I want to process HiChIP data, but cannot find any reference ChIP-seq file. What should I do?
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>