Fit-Hi-C

Ferhat Ay, Timothy L. Bailey, William S. Noble. 2014. "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts." Genome Research. 24(6):999-1011, 2014. (Supplementary information)

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Documentation

Source code

This software is offered under an MIT license. For details: http://opensource.org/licenses/MIT Copyright (c), 2012, University of Washington.

Bioconductor

An R implementation of Fit-Hi-C is available via Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/FitHiC.html.

Pre-processed input data sets

See How to run Fit-Hi-C for descriptions of the various file formats used below.

   Hi-C library / Citation       Raw contact counts  
(.gz)   		    Fragment lists  
(.gz)   		    ICE 1 biases per  
locus (.gz)    		   Contact confidences  
(.gz)   		    Fit-Hi-C report  
(.html)   
Yeast - HindIII 2 1 RE - 5 RE 1 RE - 5 RE 1 RE - 5 RE 1 RE Plots from spline-2 at 1 RE resolution
Yeast - EcoRI 2 1 RE - 5 RE 1 RE - 5 RE 1 RE - 5 RE 1 RE
Yeast - HindIII (gDNA contr.) 2 1 RE - 5 RE 1 RE - 5 RE 1 RE - 5 RE 1 RE
Yeast - EcoRI (gDNA contr.) 2 1 RE - 5 RE 1 RE - 5 RE 1 RE - 5 RE 1 RE
GM06990 - HindIII 3 50 RE - 100 RE 50 RE - 100 RE 50 RE - 100 RE 50 RE Plots from spline-2 at 50 RE resolution
GM06990 - NcoI 3 50 RE - 100 RE 50 RE - 100 RE 50 RE - 100 RE 50 RE
K562 - HindIII 3 50 RE - 100 RE 50 RE - 100 RE 50 RE - 100 RE 50 RE
Human IMR90 - HindIII 4 10 RE - 50 RE 10 RE - 50 RE 10 RE - 50 RE 10 RE Plots from spline-2 at 10 RE resolution
Human H1-ESC - HindIII 4 10 RE - 50 RE 10 RE - 50 RE 10 RE - 50 RE 10 RE
Mouse Cortex - HindIII 4 10 RE - 50 RE 10 RE - 50 RE 10 RE - 50 RE 10 RE
Mouse ESC - HindIII 4 10 RE - 50 RE 10 RE - 50 RE 10 RE - 50 RE 10 RE
Mouse ESC - NcoI 4 10 RE - 50 RE 10 RE - 50 RE 10 RE - 50 RE 10 RE 


1 Imakaev M, et al. 2012. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9: 999–1003.
2 Duan Z, et al. 2010. A three-dimensional model of the yeast genome. Nature 465: 363–367.
3 Lieberman-Aiden E, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289–293.
4 Dixon JR, et al. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376–380.

Other links

Plasmodium 3D: Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Support

For questions about the use of Fit-Hi-C method, to request pre-processed Hi-C data or additional features and scripts, or to report bugs and provide feedback please e-mail Ferhat Ay.

Ferhat Ay < ferhatay at lji dot org >