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analysis: fun


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, December 10 – December 11, 2018

Download course materials
v2.00 6 Dec 2018
Download PDF slides
v2.00 6 Dec 2018

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.

sessions / day.1

Getting started with Circos: Yeast and Ebola

Monday 10 December 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

Circos case studies

Tuesday 11 December 2018 — Day 2

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 — Creating an image montage

sessions / day.3

Visualizing and Parsing clustal alignments

Additional material — 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

Visualizing and parsing .maf alignments

Additional material — Day 4

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