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Trance opera—Spente le Stellebe dramaticmore quotes

In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017

bioinformatics + data visualization

Learning Circos

Bioinformatics and Genome Analysis

Institut Pasteur Tunis Tunisia, September 10 – December 14, 2018

Download course materials
v1.00 21 Oct 2018

A 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.

Quick links

Course website | Circos documentation best practices getting started | Brewer palette swatches | Color resources | Points of View | Points of Significance

Daily feedback

During each day, keep track of your questions to me in a plain-text file (e.g. ~/circos.questions.day.1.txt) with one question per line, separated by a blank line. At the end of the day, have someone who has read permission to all directories concatenate these files

 cat /home/*/circos.questions.day.1.txt > circos.questions.day.1.all.txt

and email these to martink@bcgsc.ca. I will post the answers in the Updates section.

sessions / day.1

Getting started with Circos: Yeast and Ebola

Monday 22 October 2018 — Day 1

9h00 - 10h30 | Lecture 1 — Introduction to Circos

11h00 - 12h30 | Lecture (practical) 2 — Visualizing gene distribution and size in Yeast: the histogram data track

14h00 - 15h30 | Lecture (practical) 3 — Conservation in Yeast: the link data track

16h00 - 18h00 | Lecture (practical) 4 — Visualizing an Ebola strain

sessions / day.2

Visualizing and parsing .maf alignments

Tuesday 23 October 2018 — Day 2

9h00 - 10h30 | Lecture 1 — Perl data structure and regular expression refresher

11h00 - 12h30 | Lecture (practical) 2 — Parsing .maf Ebola strain alignments on the command line

14h00 - 15h30 | Lecture (practical) 3 — Parsing .maf Ebola strain alignments with Perl

16h00 - 18h00 | Lecture (practical) 4 — Visualizing Ebola strain alignments

sessions / day.3

Visualizing and Parsing clustal alignments

Wednesday 24 October 2018 — Day 3

9h00 - 10h30 | Lecture 1 — Visualization strategies

11h00 - 12h30 | Lecture (practical) 2 — Parsing clustal alignments on command line

14h00 - 15h30 | Lecture (practical) 3 — Parsing clustal alignments with Perl

16h00 - 18h00 | Lecture (practical) 4 — Plotting clustal alignments

sessions / day.4

Circos case studies

Thursday 25 October 2018 — Day 4

9h00 - 10h30 | Lecture 1 — Drawing the human genome

11h00 - 12h30 | Lecture (practical) 2 — Downloading and drawing human genes

14h00 - 15h30 | Lecture (practical) 3 — Downloading and drawing segmental duplications

16h00 - 18h00 | Lecture (practical) 4 — Flexible time