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.
9 — Recipes
1. Microbial Genome
Circos is suitable for creating images of genomes that only have one chromosome, such as circular bacterial genomes. This example mentions a few tips in creating such images.
structures crossing origin
First, and perhaps ironically, Circos doesn't actually understand the concept of a circular chromosome. In other words, a chromosome, which is represented by one or more ideograms, must have a beginning and an end which are explicitly defined.
This means that on circular chromosomes, structures (e.g. clone,
gene) that cross the origin must be defined by two entries. For
example, if you have a 1 Mb genome, and wish to have a highlight from
950,000 to 50,000 you must define two highlights: 950,000-1,000,000
and then another 1-50,000.
ideogram breaks
To achieve an image with an ideogram that appears circular, set the
ideogram spacing values to 0. This is done in the
<ideogram><spacing> found in the ideogram.conf file
(which is linked to the main circos.conf file via the <<include ideogram.conf>> directive.
<ideogram> <spacing> default = 0u break = 0u </ideogram> </spacing>
If you would like to decompose the chromosome into multiple ideograms, you still need to maintain a zero-separation between the ideograms containing the end and beginning of the chromosome. One of the images in this example shows how to introduce three axis breaks into the image in this manner, using the <pairwise> block.