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
pyGenomeTracks works with python 2.7 and python 3.6.
Currently, the best way to install pyGenomeTracks is with anaconda
$ conda install -c bioconda pygenometracks
Also, pyGenomeTracks can be installed using pip
$ pip install pyGenomeTracks
If the latest version wants to be installed use:
$ pip install git+https://github.com/maxplanck-ie/pyGenomeTracks.git
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:
$ 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:
$ pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 -o nice_image.pdf
pyGenomeTracks is used by HiCExporer and HiCBrowser (See e.g. Chorogenome navigator which is made with HiCBrowser)