Get Your Learning Organized
The Circos course was presented at the 2010 Bioinformatics and Comparative Genome Analysis workshop at the Paris Pasteur Institute.
The course is composed of four sessions: a theory lecture and three practical sessions. The practical sessions focus on the core set of Circos' features. In Session 2, you learn how to define karyotypes, and how to draw, arrange, crop, order and scale ideograms. Session 3 uses the image created in Session 2 to show how to layer 2D tracks and introduces links and rules. Session 4 demonstrates the use of rules to dynamically format and layer link and scatter plot data.
The tutorials act as documentation — each lesson presents a specific feature of Circos.
Once you download and install Circos,
# install circos > tar xvfz circos-x.xx.tgz > cd circos-x.xx
try creating the example image that ships with the Circos core distribution.
> cd example # on UNIX systems (see README for Windows use) > ./run
You will need to download the tutorials separately. Follow the installation instructions in the archive file.
> cd tutorials/2/2 # now try tutorial 2.2 > ../../../bin/circos -conf ./circos.conf
In each tutorial directory (e.g.
tutorials/2/2), there will be several configuration files (
*.conf). There will always be a
circos.conf file — this is the central configuration file that you pass to the Circos binary with the
-conf flag. There may be other variants of the central configuration file (e.g.
circos-2.conf) — these illustrate other aspects of the features discussed in the tutorial.
The first thing you will need is the karyotype for your genome. The karyotype defines the chromosomes (name, size, color) and, optionally, the cytogenetic band pattern. You can obtain karyotypes for many genomes from the
cytoBandIdeo table (UCSC genome browser).