Set of programs to process, analyze and visualize Hi-C data
Project description
Standalone program and library to plot beautiful genome browser tracks
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:
bigwig
bed (many options)
bedgraph
links (represented as arcs)
The configuration file for this image is [here](https://github.com/maxplanck-ie/pyGenomeTracks/blob/master/pygenometracks/tests/test_data/browser_tracks.ini)
Installation
Currently, the best way to install pyGenomeTracks is
`bash $ pip install git+https://github.com/maxplanck-ie/pyGenomeTracks.git `
Usage
To run pyGenomeTracks a configuration file describing the tracks is required. The easiest way to create this file is using make_tracks_file which setups up a file with defaults that can be easily changed. The format is:
`bash $ make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini `
make_tracks_file uses the file ending to guess the file type.
Then, a region can be plotted using:
`bash $ pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 -o nice_image.pdf `
pyGenomeTracks is used by [HiCExporer](https://hicexplorer.readthedocs.io/) and [HiCBrowser](https://github.com/maxplanck-ie/HiCBrowser) (See e.g. [Chorogenome navigator](http://chorogenome.ie-freiburg.mpg.de/) which is made with HiCBrowser)
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