hicAverageRegions (version 3.7.2+galaxy0)

Matrix to compute on:

Regions to average:

BED file which stores a list of regions that are summed and averaged.

List of chromosomes or a BED file containg regions:

Upstream range:

Downstream range:

Define start value of range:

If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range.

Consider strand direction:

This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1].

Average regions

This tool sums Hi-C contacts around given reference points and computes their average. This tool is useful to detect differences at certain reference points, TAD boundaries for instance, between samples.

WARNING: This tool can only be used with fixed bin size Hi-C matrices. No guarantees how and if it works on restriction site interaction matrices.

Use the output to plot the average with hicPlotAverageRegions.

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