A 2- or 4-day practical mini-course in Circos, command-line parsing and scripting. This material is part of the Bioinformatics and Genome Analysis course held at the Institut Pasteur Tunis.
BCGA 2018 | 1-day Circos course | Circos documentation best practices getting started | Brewer palette swatches | Color resources | Nature Methods Points of View Points of Significance
I'll be posting corrections to any errors in the material and answers to your questions here, as they come up.
To create an SVG file (in addition to PNG) use -svg,
> circos -svg
You can view the SVG file with Inkscape. You may want to install the CMU fonts (same as those used in Latex) that come with Circos (see etc/fonts/modern), which are the same fonts used in the PNG files.
I've added an example that shows how to parse sequence alignments and pull out SNPS in Day 1 Lecture 4.
Starting with a file like this
AGACGCGTCGTTGTT AGACTCGTCGTTGTT TCAACAATAGCTTTC TCAACAATAGCTTTC GACATTCTTACCGCA GAGATTCTTACCGGA
We get a list of SNPs (where the two records are different) by position.
4 T G 32 G C 43 C G
I've added section 5 to Day 2 Lecture 4, which shows you how to draw a Tunesian mosaic. You can use this image for your souvenir image, instead of the 9-panel example from section 4.