hicPlotViewpoint (version 3.7.6+galaxy1)

Matricies to compute on:

Region of the genome to limit the operation:

The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500

Reference point:

The format is chr:referencePoint or chr:regionStart-regionEnd.

Create bedgraph file with interactions:

Image output format:

Plot Viewpoint

hicPlotViewpoint plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data. This plotting method allows to make long-range interactions more visible.

Usage

This tool must be used on Hi-C contact matrices corrected using hicCorrectMatrix.

Output

hicPlotViewpoint outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.

/repository/static/images/1282b98dc31fd41e/pulication_plots_viewpoint.png

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