The perl script plotCGIgene_cgatools1-3.pl will create a pretty plot of a single gene overlapping a lot of CGI data (see attached LIPI.png file for LIPI gene from NA19240). Perl script needs to be run with the R program plotCGIgene.R.
The plots that are created are PDFs and require some UCSF tracks. In the future this will be changed to refseq to match CGI annotation. This script will only work with mastervar files generated from cgatools 1.3 . In the future, this will be updated to the new mastervar file generated from CGATM Tools 1.4.
Note: This script is not compatible with genomes processed with Assembly Pipeline v2.0.
Download the tool here.