Frequently asked question

How do I cite FitHiChIP?

FitHiChIP should be cited as:

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>

I do not know anything about HiChIP. What should I do?

In addition to read the FitHiChIP paper, users are requested to read the following papers for a detailed understanding of HiC and HiChIP protocols.

HiChIP protocol papers:

Hi-C related basic papers:

HiC-pro paper:

FitHiC paper (for significant interaction calling from Hi-C data)

How to install HiC-pro in the system?

HiC-pro is available through GitHub <https://github.com/nservant/HiC-Pro> (corresponding documentation is available in <http://nservant.github.io/HiC-Pro/>). The simple way is to either download GitHub archieve in a zipped format, or to clone the repository. Then, user needs to perform the following steps:

  1. (Extract the zipped archieve if downloaded.) Go to the directory containing HiC-pro (generally inside the folder name HiC-Pro-master)

  2. Edit the file config-install.txt by specifying the path names of required packages.

  3. Type make configure in the command line, and press enter.

  4. Once configuration is performed, type make CONFIG_SYS=config-install.txt install in the command line, and press enter. Successful execution of this command would install HiC-pro in a folder named HiC-Pro_*VERSIONNAME*

How to visualize the FitHiChIP loops in genome browser?

FitHiChIP produces output loops compatible to different epigenome browsers. They are: WashU epigenome browser, UCSC genome browser, and IGV browser.

For details, please check the page Details of FitHiChIP outputs for a detailed description.

What type of input data formats are supported in FitHiChIP?

FitHiChIP supports multiple input data formats: 1) HiC-pro generated valid pairs, 2) .hic file, 3) .cool file, 4) text file containing chromosomal interacting pairs and contact counts.

For details, see the page Setting up configuration file.

What type of HiChIP interactions are supported in FitHiChIP?

Currently FitHiChIP supports finding statistically significant CIS interactions. The foreground (output interaction type) depends on the option IntType (see Setting up configuration file). Default mode of FitHiChIP is to report peak-to-all interactions (one end is a peak, while the other end may or may not be a peak).

Does FitHiChIP support processing HiC data?

Yes, user can provide any HiC contact map according to the parameter and file specifications provided in Setting up configuration file. Note that the parameter IntType should be specified as 4 (ALL-to-ALL). No ChIP-seq peak information is required in this case. The ICE bias regression (BiasType = 2), and FitHiChIP loose background (UseP2PBackgrnd = 0) is preferable in processing HiC datasets.

I want to process HiChIP data, but cannot find any reference ChIP-seq file. What should I do?

ChIP-seq peak information can be also obtained from the HiChIP data itself, by employing the peak calling routine provided in FitHiChIP. For details, please check the HiChIP peak calling routine in the page Various utility scripts / functions.

Does FitHiChIP support processing Capture-HiC data?

Yes, please check the page Various utility scripts / functions, specifically (8. Applying FitHiChIP on capture HiC data).