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.
In this example, I use local scale adjustment to draw attention to regions of chromosomes 1 and 2 in an image that contains sparse data.
The benefit of using scale adjustments is that the data domain is not cropped and therefore all data points are plotted.