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 tutorial, I'll cover how to embed highlight parameters in your highlight data file. This is a convenient way of formatting highlights because generation of the parameters can be incorporated into your data analysis and reporting pipeline.
Using the genes.txt file used in the previous section, I added a random fill color (red, green, blue, purple, yellow, orange, grey) to each entry. For entries that received a red color, I adjusted the radial start/end positions to be closer to the center of the circle than other colors. For entries that received a green color, I similiarly adjusted r0,r1 to format these entries to fall outside of the circle.
Here is an excerpt of the data file, with the additional formatting option fields.
hs1 1298972 1300443 fill_color=blue hs1 1311738 1324571 fill_color=red,r0=0.6r,r1=0.6r+50p hs1 1397026 1421444 fill_color=green,r0=1.1r,r1=1.15r hs1 1437417 1459927 fill_color=green,r0=1.1r,r1=1.15r hs1 1540746 1555847 fill_color=yellow hs1 1560962 1645635 fill_color=purple hs1 1624179 1645623 fill_color=grey
The configuration block for this highlight set defines a default r0,r1 value, which applies to any entries in the data file that don't have overriding r0,r1 values. Thus, most of the highlights fall between r0,r1 = 0.7r,0.7r+200p, with the red and green entries shifted inward and outward in the circle, respectively.
All of the other highlight parameters may be specified in a similar manner in the data file.