First edit the sim.cfg file.
Next run gsim:
this will generate files:
Next run dsim:
This will generate files
These files map gene identifiers (which are the integers 0, 1, 2, ...) to intensities, one "array" per file.
To view the distributions run gene_expression_plotter.pl, which takes two arguments, the list of files for group1 and the list of files for group 2. These are generated automatically when you run dsim and are saved to Afiles and Bfiles. The distributinos are written to standard out. For each gene three distributions are written, the first combines both groups, the second gives group 1 and the thrid gives group 2.
> perl gene_expression_simulator.pl Afiles Bfiles > distributions.txt