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:
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 consideres as treatment vs control in 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 BACKGROUNDMODELFILE [--threads THREADS] [--averageContactBin AVERAGECONTACTBIN] [--writeFileNamesToFile WRITEFILENAMESTOFILE] [--fixateRange FIXATERANGE] [--outputFolder OUTPUTFOLDER] [--help] [--version]
- --matrices, -m
Path to the Hi-C matrices which store the captured Hi-C data per sample.
Defines the region upstream and downstream of a reference point which should be considered in the analysis. Please have in mind to use the same fixate range setting as it was for the background model computation and that distances of the range larger as 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 per line one reference point
- --backgroundModelFile, -bmf
path to the background file computed by chicViewpointBackgroundModel
- --threads, -t
Number of threads. Using the python multiprocessing module.
Average the contacts of n bins via sliding window approach to smooth the values and be less sensitive for outlieres..
- --writeFileNamesToFile, -w
Set this parameter to have a file with all file names of the viewpoint files, useful only for batch processing mode.
- --fixateRange, -fs
Fixate range of backgroundmodel starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.
- --outputFolder, -o
This folder contains all created viewpoint files.
show program’s version number and exit