Getting Started
Don't know where to start? Start here!
Installation
First, download and install Circos. If you are a Windows user, please read the UNIX vs Windows tutorial, especially if you are not familiar with the command line.
If you run into problems, first make sure you have all necessary Perl modules. If you are certain that all modules are installed and functioning, use the Google Group to search for similar problems or post a question to the community.
Generate Example Image
To verify that Circos has been installed correctly, generate the example image. This is a complex image which will take about 1 minute to generate.
On UNIX (e.g. Linux), from the Circos installation directory
# UNIX > cd example > ./run # batch file runs 'circos -conf etc/circos.conf' debuggroup summary 0.86s parsing karyotype and organizing ideograms debuggroup summary 1.08s applying global and local scaling debuggroup summary 1.15s allocating image, colors and brushes debuggroup summary 7.19s drawing highlights and ideograms debuggroup summary 8.94s processing links debuggroup summary 13.31s processing data tracks Processing text track - this might take a while debuggroup summary 68.75s generating output created image at ./circos.png created image at ./circos.svg # look at circos.png
On Windows, from the Circos installation directory
# Windows
> cd example
> perl ..\bin\circos -conf etc\circos.conf
You can always leave out the -conf etc\circos because Circos will find it automatically.
> perl ..\bin\circos
If you get a "configuration file not found" error, then you are very likely not in the example directory. To check, use cd which will report the current directory. It should be where you installed circos.
> cd C:\circos\example
Tutorials and Documentation
Circos documentation is available as a series of online tutorials which describe all of the features in Circos in a logical progression.
quick start
If you are impatient and want the shortest route to creating an image, read the Quick Guide tutorials. This is a series of 8 tutorials that show you how to build up an image from scratch, using data displayed on the human genome chromosomes.
best practices
It's not always clear how to proceed when you're starting out. Refer to the Circos Best Practices guide for tips to make your configuration modular and streamlined.
legacy configuration files
Many users experience issues caused by using new versions of Circos with old configuration files. If you are getting started, always use the newest version of Circos.
extended tutorials
The data and configuration files for all online tutorials can be downloaded as a separate package. If one of the tutorials can act as a template for your image, use it as a starting point.
support
Direct your Circos questions (installation, configuration, best practices) to the Google Group.
Using Circos in Publications
If you are considering using Circos for a figure in a publication or magazine, look through published images for inspiration.
- Circos can be used to visualize genomic data
- Circos can be used to visualize any other data, such as debates, bus schedules, relationships, social network, network traffic, and things we haven't though of
- Circos requires Perl to run
- Circos does not have a user interface—it is controlled through a plain-text configuration file
- Circos can be easily automated
- Circos can generate SVG files which you can post-process in Illustrator or Inkscape
If you are close to publication, I am happy to help you design and/or refine your image. I've done it many times before—drop me a line and we'll get started.
Using Circos as Art
If you like things round, and distrust things square, Circos can be a platform for visual expression.
It has been used artistically before, perhaps most prominently in the David Cronenberg Chromosomes exhibit, where I collaborated with Volumina to give the book and exhibit a scientific feel.