This tool considers the first 1,000,000 reads (or user defined number) of the mapped bam files to get a quality estimate of the Hi-C data.


The tool hicQuickQC considers the first n lines of two bam/sam files to get a first estimate on the quality of the data.

usage: hicQuickQC --samFiles two sam files two sam files --QCfolder FOLDER
                  (--binSize BINSIZE | --restrictionCutFile BED file)
                  [--restrictionSequence RESTRICTIONSEQUENCE]
                  [--danglingSequence DANGLINGSEQUENCE] [--lines LINES]
                  [--help] [--version]

Required arguments

--samFiles, -s

The two PE alignment sam files to process


Path of folder to save the quality control data for the matrix. The log files produced this way can be loaded into hicQC in order to compare the quality of multiple Hi-C libraries.

Optional arguments

--binSize, -bs

Size in bp for the bins. The bin size depends on the depth of sequencing. Use a larger bin size for libraries sequenced with lower depth. Alternatively, the location of the restriction sites can be given (see –restrictionCutFile). Optional for mcool file format: Define multiple resolutions which are all a multiple of the first value. Example: –binSize 10000 20000 50000 will create a mcool file formate containing the three defined resolutions.

Default: 10000

--restrictionCutFile, -rs

BED file with all restriction cut places (output of “findRestSite” command). Should contain only mappable restriction sites. If given, the bins are set to match the restriction fragments (i.e. the region between one restriction site and the next).

--restrictionSequence, -seq

Sequence of the restriction site.


Sequence left by the restriction enzyme after cutting. Each restriction enzyme recognizes a different DNA sequence and, after cutting, they leave behind a specific “sticky” end or dangling end sequence. For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. For DpnII, the restriction site and dangling end sequence are the same: GATC. This information is easily found on the description of the restriction enzyme. The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol.


Number of lines to consider for the qc test run.

Default: 1000000


show program’s version number and exit

For more information see encode .