hicDetectLoops can detect enriched interaction regions (peaks / loops) based on a strict candidate selection, negative binomial distributions and Anderson-Darling / Wilcoxon rank-sum tests.

The algorithm was mainly develop on GM12878 cells from Rao 2014 on 10kb and 5kb fixed bin size resolution.

Example usage

$ hicDetectLoops -m matrix.cool -o loops.bedgraph --maxLoopDistance 2000000 --windowSize 10 --peakWidth 6 --pValuePreselection 0.05 --pValue 0.05 --peakInteractionsThreshold 20 --maximumInteractionPercentageThreshold 0.1 --statisticTest anderson-darling

The candidate selection is based on the restriction of the maximum genomic distance, here 2MB. This distance is given by Rao 2014. For each genomic distance a negative binomial distribution is computed and only interaction pairs with a threshold less than --pValuePreselection are accepted. Detected candidates need to have at least an interaction count of --maximumInteractionPercentageThreshold times the maximum value for their genomic distance. Please note that --maximumInteractionPercentageThreshold was introduced with HiCExplorer release 3.2. Earlier versions did not have this parameter yet and therefore their outputs may differ. In a second step, each candidate is considered compared to its neighborhood. This neighborhood is defined by the --windowSize parameter in the x and y dimension. Per neighborhood only one candidate is considered, therefore only the candidate with the highest peak values is accepted. As a last step, the neighborhood is split into a peak and background region (parameter --peakWidth). The peakWidth can never be larger than the windowSize. However, we recommend for 10kb matrices a windowSize of 10 and a peakWidth of 6.

The output file (´´-o loops.bedgraph``) contains the x and y position of each loop and its corresponding p-value of the Anderson-Darling test.

1   120000000       122500000       1       145000000       147500000       0.001

The results can visualized using hicPlotMatrix:

$ hicPlotMatrix -m matrix.cool -o plot.png --log1p --region 1:18000000-22000000 --loops loops.bedgraph

Computes enriched regions (peaks) or long range contacts on the given contact matrix.

usage: hicDetectLoops --matrix MATRIX --outFileName OUTFILENAME
                      [--peakWidth PEAKWIDTH] [--windowSize WINDOWSIZE]
                      [--pValuePreselection PVALUEPRESELECTION]
                      [--peakInteractionsThreshold PEAKINTERACTIONSTHRESHOLD]
                      [--maximumInteractionPercentageThreshold MAXIMUMINTERACTIONPERCENTAGETHRESHOLD]
                      [--pValue PVALUE] [--maxLoopDistance MAXLOOPDISTANCE]
                      [--minLoopDistance MINLOOPDISTANCE]
                      [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                      [--region REGION] [--threads THREADS]
                      [--statisticalTest {wilcoxon-rank-sum,anderson-darling}]
                      [--help] [--version]

Required arguments

--matrix, -m

The matrix to compute the loop detection on.

--outFileName, -o

Outfile name to store the detected loops. The file will in bedgraph format.

Optional arguments

--peakWidth, -pw

The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins.

--windowSize, -w

The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins

--pValuePreselection, -pp

Only candidates with p-values less the given threshold will be considered as candidates. For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given. This does NOT influence the p-value for the neighborhood testing.

Default: 0.05

--peakInteractionsThreshold, -pit

The minimum number of interactions a detected peaks needs to have to be considered.

Default: 5

--maximumInteractionPercentageThreshold, -mip

For each distance the maximum value is considered and all candidates need to have at least ‘max_value * maximumInteractionPercentageThreshold’ interactions.

Default: 0.01

--pValue, -p

Rejection level for Anderson-Darling test for H0. H0 is peak region and background have the same distribution.

Default: 0.05


Maximum genomic distance of a loop, usually loops are within a distance of ~2MB.

Default: 2000000


Minimum genomic distance of a loop to be considered.

Default: 100000


Chromosomes to include in the analysis. If not set, all chromosomes are included.


The format is chr:start-end.

--threads, -t

Number of threads to use, the parallelization is implemented per chromosome.

Default: 4

--statisticalTest, -st

Possible choices: wilcoxon-rank-sum, anderson-darling

Which statistical test should be used.

Default: “anderson-darling”


show program’s version number and exit