HiCExplorer tools

tool

type

input files

main output file(s)

application

hicFindRestSites

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 or Knight-Ruiz 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

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, minimum, 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.

hicQuickQC

information

2 BAM/SAM files

An estimated quality control report

Estimated quality report of the Hi-C data.

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

hicDetectLoops

analysis

one Hi-C matrices

bedgraph file with loop locations

Detects enriched regions. Visualization with hicPlotmatrix and –loop parameter.

hicValidateLocations

analysis

one loop, one protein peak file

bedgraph file with matched loop locations, one file with loop / protein statistics

Matches loop locations with protein peak positions

hicMergeLoops

analysis

multiple loop files

bedgraph file with merged loop locations

Merges detect loop locations of different resolutions

hicCompartmentalization

visualization

one Hi-C interaction matrix one PCA bedgraph file

one image polarization plot

The global compartmentalization signal.

hicPlotAverageRegions

visualization

one npz file

one image

Visualization of hicAverageRegions.

:ref`hicPlotSVL`

analysis

one / multiple Hi-C matrices

one image, p-values file, raw data file

Computes short/long range contacts; a box plot, a p-value and raw data file

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.

chicQualityControl

preprocessing

Hi-C matrices reference point BED file

two plots accepted reference point BED file

Checks for sparsity of viewpoints and removes them if too sparse.

chicViewpointBackgroundModel

preprocessing

Hi-C matrices reference point BED file

background model file

Creates a background model for all given samples and reference points.

chicViewpoint

preprocessing

Hi-C matrices background model file

viewpoint file(s)

Creates per sample per viewpoint one viewpoint file.

chicSignificantInteractions

chicAggregateStatistic

preprocessing analysis

viewpoint file(s) background model file

significant interaction file(s) target file(s)

Detects significant interactions per viewpoint based on the background and neighborhood merging via x-fold and loose p-values.

preprocessing

viewpoint files(s) target file (s)

aggregated file(s) for differential test

Aggregates for one viewpoint of two samples via a target file the locations to test for differential interactions.

chicDifferentialTest

analysis

aggregated file(s) of two samples

H0_accepted-, H0_rejected-files

Tests with chi2 or fisher for differential interactions of two samples.

chicPlotViewpoint

visualization

viewpoint file(s) differential expression file(s) significant interactions file(s)

one image per viewpoint

Visualization of a viewpoint.

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).