chicViewpoint¶

Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by –outputFolder, and 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.bed

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

An example usage is:

$chicViewpoint –matrices matrix1.cool matrix2.cool matrix3.cool –referencePoints referencePointsFile.bed –range 20000 40000 –outputFolder interactionFilesFolder An example usage for batch mode is:$ chicViewpoint –matrices matrix1.cool matrix2.cool matrix3.cool –referencePoints referencePointsFile.bed –range 20000 40000 –outputFolder interactionFilesFolder –writeFileNamesToFile interactionFile.txt

usage: chicViewpoint --matrices MATRICES [MATRICES ...] --range RANGE RANGE
--referencePoints REFERENCEPOINTS --backgroundModelFile
[--averageContactBin AVERAGECONTACTBIN]
[--writeFileNamesToFile WRITEFILENAMESTOFILE]
[--fixateRange FIXATERANGE] [--allViewpointsList]
[--outputFolder OUTPUTFOLDER] [--help] [--version]


Required arguments¶

--matrices, -m

Path to the Hi-C matrices which store the captured Hi-C data per sample.

--range

Defines the region upstream and downstream of a reference point which should be considered in the analysis. Please remember to use the same fixate range setting as for the background model computation and that distances of the range larger than the fixate range use the background model of those.Format is –region upstream downstream

--referencePoints, -rp

Reference point file. Needs to be in the format: ‘chr 100’ for a single reference point or ‘chr 100 200’ for a reference region and with a single reference point per line

--backgroundModelFile, -bmf

path to the background file computed by chicViewpointBackgroundModel

Optional arguments¶

Number of threads (uses the python multiprocessing module).

Default: 4

--averageContactBin

Average the contacts of n bins via a sliding window approach to smooth the values and be less sensitive for outliers.

Default: 5

--writeFileNamesToFile, -w

Set this parameter to have a file with all file names of the viewpoint files (useful only in batch processing mode).

--fixateRange, -fs

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

Default: 500000

--allViewpointsList, -avl

Writes a file where all viewpoints all samples are sorted by the viewpoints.

Default: False

--outputFolder, -o

This folder contains all created viewpoint files.

Default: “interactionFiles”

--version

show program’s version number and exit