IGV

Overview

  • Introduction to IGV.
    • What is IGV.
    • How to run IGV.
  • Navigating IGV.
    • The IGV user interface.
    • Moving around genomes.
  • Loading and visualising data.
    • Genome information and annotation.
    • User supplied data.
    • Sample information.
    • External data.
  • Displaying genomics data
    • Basic visualisation.
    • Data dependent visualisation.

What is IGV?

  • Created by the Broad institute.
  • Genome browser.
    • Visualises genomic data (expression, ChIP, resequencing, multiple alignment, shRNA).
    • Handles most common genomic data types.
    • Java Desktop application
    • No dependence on server.
    • Loads data locally or from URL, consumes memory and CPU.

How to run IGV?

  • Requires Java
  • IGV available from Broad