HiC-Pro is designed to process Hi-C data from .fastq files to normalized contact matrices. Additional software or methods should then be used to perform downstream analysis. We therefore decided to propose several utilities to increase the compatibility of HiC-Pro with other tools. Most of the scripts presented below were developed by HiC-Pro users or collaborators. Many thanks to them for sharing their work with us, and do not hesitate the contact us with many new ideas !
Since v2.11.0, HiC-Pro is compatible with the MultiQC tool, allowing in a simple and dynamic way to have a nice report summarizing your HiC-Pro analysis. To do so, simply run:
cd HIC-PRO_OUTPUT
multiqc .Example of multiQC reports are available here.
The Juicebox software allows dynamic visualization of HiC contact maps. The list of valid interaction products called by HiC-Pro can can be converted in Juicebox input format (.hic file). To do so, please have a look at the hicpro2juicebox.sh utility.
HiC-Pro is also compatible with the higlass visualization software. The matrix files or the list of valid interactions can be used by the hicpro2higlass.sh utility to generate higlass input files (.cool). Please look at the utility page page for details about how to use it.
The output format of HiC-Pro can be loaded into the HiCPlotter software for Hi-C data visualization. Here is a small example of how to use it.
## Plot the genome-wide map at 1Mb resolution
python HiCPlotter.py -f hic_results/matrix/sample1/iced/1000000/sample1_1000000_iced.matrix -o Examplegw -r 1000000 -tri 1 -bed hic_results/matrix/sample1/raw/1000000/sample1_1000000_ord.bed -n hES -wg 1 -chr chrX
## Plot the chrX at 150Kb resolution
python HiCPlotter.py -f hic_results/matrix/sample1/iced/150000/sample1_150000_iced.matrix -o Exemple -r 150000 -tri 1 -bed hic_results/matrix/sample1/raw/150000/sample1_150000_ord.bed -n Test -chr chrX -ptr 1TADs calling is frequently run on Hi-C data at a 40Kb or higher resolution. In order to run the first method proposed by Dixon et al., you can generated the input file using the sparseTodense.py utility.
TADtool is an interactive tool for the identification of meaningful parameters in topologically-associating domains (TADs) algorithms for Hi-C data. Both insulation scores and directionality indexes are implemented.
Matrix files in triplet sparse format generated by HiC-Pro can be easily loaded into TADtool.
Fit-Hi-C is a popular approach to detect significant interaction on intra-chromosoml contact map. Please use the hicpro2fithic.py utility to connvert HiC-Pro output to Fit-Hi-C input files.
The HiTC package proposes function to import HiC-Pro output into the R environment. Contact matrices are then stored as sparse Matrix, which can be used for any downstream analysis.