Circos > Documentation

Tutorials and Course

The tutorials serve as a walkthrough and documentation for Circos. The course is a more structured set of materials that takes you through creating several images from scratch.

Example Image

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

Creating a Tutorial Image

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.

Creating Your Own Image

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).

You can download the karyotype from the table browser or directly for human hg19 (Feb 2009) hg18 (Mar 2006), mouse mm9 (Jul 2009) mm8 (Mar 2006), rat rn4 (Nov 2004) rn3 (Jun 2003), or other species.

Once you have decided which ideograms to draw (ideograms are the graphical representation of chromosomes), add highlights, 2D tracks and links.