chicViewpoint (version 3.7.5+galaxy0)

Matricies to compute on:

Reference points:

Bed file contains all reference points which should be used to create viewpoints.

Upstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Downstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Background model:

The background file computed by chicViewpointBackgroundModel

Average contacts window size:

Average the contacts of n bins via a sliding window approach.

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.

Compute viewpoints for all given reference points

Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by --outputFolder, the files are named by the name of the reference point, the sample name and the location of the reference point:

gene_matrix_name_chr_start_end.txt

If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate --writeFileNamesToFile. In this file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.

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