Starting usage

To run pyGenomeTracks a configuration file describing the tracks is required.

In a configuration file, each track is defined as a block of parameters starting with its name [track name] and continues with the parameters for that track such as the file location, its title, height, color etc.

The tracks are then plotted in the order of the configuration file from top to bottom.

The easiest way to create this file is using the program make_tracks_file which creates a configuration file with defaults that can be easily changed. make_tracks_file uses the file ending to guess the file type. Then, a region can be plotted using pyGenomeTracks. Both programs are described below:


Facilitates the creation of a configuration file for pyGenomeTracks. The program takes a list of files and does the boilerplate for the configuration file.

usage: make_tracks_file --trackFiles <bigwig file> <bed file> etc. -o tracks.ini

Named Arguments

--trackFiles, -f

Files to use in for the tracks. The ending of the file is used to define the type of track. E.g. .bw for bigwig, .bed for bed etc. For a arcs or links file, the file ending recognized is .arcs or .links

--out, -o

File to save the tracks


show program’s version number and exit