HiCExplorer tools

tool type input files main output file(s) application
findRestSites preprocessing 1 genome FASTA file bed file with restriction site coordinates Identifies the genomic locations of restriction sites
hicBuildMatrix preprocessing 2 BAM/SAM files hicMatrix object Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads
hicCorrectMatrix preprocessing hicMatrix object normalized hicMatrix object Uses iterative correction to remove biases from a Hi-C matrix
hicMergeMatrixBins preprocessing hicMatrix object hicMatrix object Merges consecutives bins on a Hi-C matrix to reduce resolution
hicSumMatrices preprocessing 2 or more hicMatrix objects hicMatrix object Adds Hi-C matrices of the same size
hicNormalize preprocessing multiple Hi-C matrices multiple Hi-C matrices Normalize data to 0 to 1 range or to smallest total read count
hicFindEnrichedContacts analysis hicMatrix object hicMatrix object Identifies enriched Hi-C contacts
hicCorrelate analysis 2 or more hicMatrix objects a heatmap/scatterplot Computes and visualises the correlation of Hi-C matrices
hicFindTADs analysis hicMatrix object bedGraph file (TAD score), a boundaries.bed file, a domains.bed file (TADs) Identifies Topologically Associating Domains (TADs)
hicPlotMatrix visualization hicMatrix object a heatmap of Hi-C contacts Plots a Hi-C matrix as a heatmap
hicPlotTADs visualization hicMatrix object, a config file Hi-C contacts on a given region, along with other provided signal (bigWig) or regions (bed) file Plots TADs as a track that can be combined with other tracks (genes, signal, interactions)
hicPlotDistVsCounts visualization hicMatrix object log log plot of Hi-C contacts per distance Quality control
hicConvertFormat data integration one/multiple Hi-C file formats Hi-C matrices/outputs in several formats Convert matrix to different formats
hicAdjustMatrix data integration one Hi-C file formats Hi-C matrix Removes, masks or keeps specified regions of a matrix
hicInfo information one or more hicMatrix objects Screen info Prints information about matrices, like size, maximum, minimux, bin size, etc.
hicPCA analysis one Hi-C matrix bedgraph or bigwig file(s) for each eigenvector Computes for A / B compartments the eigenvectors
hicTransform analysis one Hi-C matrix Hi-C matrix Computes a obs_exp matrix like Lieberman-Aiden (2009), a pearson correlation matrix and or a covariance matrix. These matrices can be used for plotting.
hicPlotViewpoint visualization one Hi-C matrix A viewpoint plot A plot with the interactions around a reference point or region.
hicQC information log files from hicBuildMatrix A quality control report Quality control of the created contact matrix.
hicCompareMatrices analysis two Hi-C matrices one Hi-C matrix Applies diff, ratio or log2ratio on matrices to compare them.
hicAverageRegions analysis multiple Hi-C matrices one npz object Averages the given locations. Visualization with hicPlotAverageRegions
hicPlotAverageRegions visualization one npz file one image Visualization of hicAverageRegions.
hicMergeTADbins preprocessing one Hi-C matrix, one BED file one Hi-C matrix Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix.

General principles

A typical HiCExplorer command could look like this:

$ hicPlotMatrix -m myHiCmatrix.h5 \
-o myHiCmatrix.pdf \
--clearMaskedBins \
--region chrX:10,000,000-15,000,000 \
--vMin -4 --vMax 4 \

You can always see all available command-line options via –help:

$ hicPlotMatrix --help
  • Output format of plots should be indicated by the file ending, e.g. MyPlot.pdf will return a pdf file, MyPlot.png a png-file.
  • Most of the tools that produce plots can also output the underlying data - this can be useful in cases where you don’t like the HiCExplorer visualization, as you can then use the data matrices produced by deepTools with your favorite plotting tool, such as R.
  • The vast majority of command line options are also available in Galaxy (in a few cases with minor changes to their naming).