Spring-school in Bioinformatics & Population Genomics

Practicals for the May/June 2016 Spring School in Bioinformatics & Population Genomics organized by the SIB PhD Training Network and the Staromics and Ecology-Evolution doctoral programs.

Prerequisites

We suppose that you are able at ease:

• in the command line. For a refresher, try the SIB’s UNIX fundamentals online course.
• with R. The swirl() library/course can help:
  • follow the R programming self-led course (skip the sections Simulation and Dates and Times)
  • follow at least the ggplot section of the Exploratory_Data_Analysis swirl course

Virtual Machine image

Our colleagues at Vital-IT prepared a Virtual Machine Image that contains software and data. Use it by loading it into Virtual Box. For detailed explanations and troubleshooting, check the main course info page.

It may be feasible to do some of this stuff on a your favorite cluster or your local machine. However, it will be complicated. Among other things you’ll need to install a bunch of software and data. Better to just use the Virtual Machine.

Practicals

• Reads to genome to gene predictions: Short read cleaning, genome assembly, quality control, gene prediction, quality control (Monday).
• Population sequencing to genotypes to population genetics statistics (Tuesday):
  • Mapping reads, calling variants, visualizing variant calls.
  • Analysing variants: PCA, measuring Differentiation & Diversity.
• Inferring population sizes and gene flow. (1h Wednesday)
• Gene expression:
  • From raw sequencing data to transcript expression levels. (Wednesday)
  • Gene-level clustering and differential expression analysis. (Thursday)

Authors/Credits

These practicals were put together by:

• Rodrigo Pracana

• Julien Roux www @_julien_roux

• Robert Waterhouse www @rmwaterhouse
• Stefan Schiffels @stschiff
• Yannick Wurm - www @yannick__
• with content derived from:
  • Oksana Riba-Grognuz’ contributions for the 2012 edition of this course,
  • Bruno Vieira’s contributions to QMUL’s Bioinformatics MSc version of this course.

Thanks to Robin Engler, Ivan Topolsky and Vassilios Ioannidis & Vital-IT for putting together the Virtual Machine image for this course. And big credit to Gregoire Rossier for handling all the logistics of everything.