Genome Analysis Workshop§

Announcements§

  • New: you will need your own laptop for the class. And IDEALLY it is a Mac or Linux machine. You can run Linux under VirtualBox on Windows.
  • Class size is limited to 20. We anticipate being full, so register early.
  • Tuition waivers are available for Postdocs and PRAs. You also need to fill out a non-degree application.

Course Description§

The Genome Analysis Workshop is a hands-on tutorial of skills needed to process large genomics data sets and visualize their results. The class is taught from the standpoint of a biologist with practical goals (e.g., to interpret the results of a sequencing-based experiment and gain biologically meaningful insight).

We focus on working in the Linux environment, with emphasis on command-line tools, Python programming and the R statistical computing environment. We use publicly available next-generation DNA sequencing data from the ENCODE project to illustrate standard approaches for manipulating sequencing data, aligning sequences to a reference genome, generating coverage plots and displaying them in the UCSC Genome Browser. We will cover specific analyses used in ENCODE project including ChIP-seq, DNase I footprinting, mRNA-seq and genome sequencing to identify single nucleotide variants.

Contents§

Additional Resources§

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