chicQualityControl (version 3.7.2+galaxy0)

Matricies to compute on:

Reference points:

Bed file contains all reference points which should be used to build the background model.

Sparsity threshold:

Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix.

Clip background distance:

Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.

DPI for image:

Change the default resolution of the plot.

Image output format:

Compute the quality of viewpoints

Computes the sparsity of each viewpoint to determine their quality. A viewpoint is considered of bad quality if it is too sparse i.e. there are too many locations with no interactions recorded.

This script outputs five files: A plot with the sparsity distribution per matrix, a plot with the sparsity distribution as histograms and a filtered reference points file. Additional, the raw filter data and the rejected viewpoints are returned.

An example usage is:

$ chicQualityControl -m matrix1.h5 matrix2.h5 -rp referencePointsFile.txt --range 20000 40000 --sparsity 0.01 -o referencePointFile_QC_passed.txt

For more information about HiCExplorer please consider our documentation on readthedocs.io