Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
CircosAPI is a Perl module that is written to provide users with a Perl interface to create Circos graphics.
The module generates the configuration from within Perl code, giving you the ability to incorporate Circos into your pipeline.