Integrative Genomics Viewer

The Rockefeller University

Bioinformatics Resource Centre

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

http://www.broadinstitute.org/software/igv/download

How to run IGV? (Binary version)

• Download to computer.
• Runs locally.
• Archived versions available

How to run IGV? (Webstart)

• Runs from webstart.
• Always runs latest version of IGV.

IGV GUI

IGV GUI

• Sample information panel <1>
• Genome Navigation panel <2>
• Data panel <3>
• Attribute panel <4>

Menu Bar

• File - Load data/sample information.
• Genome - Load and manage genomes.
• View -  Display preferences.
• Tracks - Group/sort/filter data tracks.
• Regions - Create region/gene lists.
• Tools -  Access to Integrated tools (IGVtools/Bedtools).
• GenomeSpace - Export/import from Genomespace

Moving around genomes

• Cytoband selection and zooming
• Scrolling
• Selection of region of interest

Whole genome view

Zooming

Scrolling

Jump to Region

“Bookmarking” regions of interest

• Regions may be added to “Regions of interest”

• These act as bookmarks for areas of particular interest

• Bookmarks can be added by -
  • Bookmarking visible window
  • Selecting region within window

Bookmarking - Visible window

“Bookmarked” Region Of Interest

Bookmarking

• Bookmarks may be created from selecting "region of interest" button and edge of region

Sequences from regions of interest

• A useful feature of "regions of interest" is to retrieve of BLAT sequences.

Sequences from regions of interest

BLAT

Viewing sequences

• At a predefined resolution, sequence information becomes available.

Viewing sequences

• Strand of sequence can be altered.
• Differing translation tables can be selected

Loading data in IGV

Loading Genome Information

• Most genomes can be selected from dropdown.

Loading Genome Information

• Genomes not included may be downloaded from repository

Loading Genome annotation

• For supported genomes, gene positions are automatically included in “feature” panel.
• Additional gene positions can be loaded into IGV in gff format.

Loading Sample data

• Most common formats can be loaded into IGV through file menu
• Acceptable data formats include:-
• BED (.bed)
• BAM and index (.bam with .bai/.bam.bai)
• BigWig (.bw)
• BedGraph/Wig (.bedGraph, .wig)
  • And many more…
  • link to IGV formats

Loading Sample Metadata

• IGV allows the inclusion of information on samples.
• Sample information is then included in sample information panel.

Example Sample information file

• http://www.broadinstitute.org/igvdata/exampleFiles/exampleSampleInfo.txt

Tracktables package.

• R/Bioconductor packages
  • Sanjay and Tom.
• Creates HTML reports with sample information for use with IGV.

Using sample information.

• Sample information can include discrete and continuous.

• Can be used to “sort” and “filter” tracks.

• Can split tracks across panels by “group”

Loading external data and annotation

Load data from a URL.

• As with UCSC, IGV supports data hosted on external servers.
• Data accessible from a URL such as HTTP and FTP can be loaded using the “Load from URL”.

Loading external data and annotation

Load data from a server

(IGV/Encode servers).

• Unlike UCSC, IGV comes with few external tracks.

• External tracks (relevant to the genome) can be loaded from the IGV server or Encode-IGV server.

Grabbing encode data directly

• Encode data can be downloaded from UCSC.
• http://genome.ucsc.edu/ENCODE/
• This however does not come with sample information provided through IGV interface

Viewing data

Viewing data

• IGV associates common file formats with default display methods.

• Most of the time IGV will make a sensible choice how we wish to display data.

Accepted formats and default display.

Information on accepted file formats and default display can be found at -

 http://www.broadinstitute.org/software/igv/RecommendedFileFormats

Bed/bigBed

• Basic
• Tab-delimited
• Chrom,Start,End
• Bed6
• bigBed (recommended)

Wig, BedGraph and BigWig

• Wig/bedGraph require high memory load
• Recommended format is bigWig

BAM alignment files

• BAM files contain alignment information.
• Require an accompanying .bai index file for display

Finer control of display

• IGV allows for customization of track display.

• Menu bar -> View -> Preferences

• Select track (right click)

Display preferences

General

Display preferences

Tracks

Display preferences

Alignments

Track display options

BAM

• Read Packing, grouping, sorting, colouring options.

Track display options
Graph/interval files

• Track colour/appearance

Track display options
Graph/interval files

• Graph type

Track display options

• Data Scaling.

• Autoscaling adjusts to track's visible signal maximum

Some cool features

IGV can display splicing information!

...and do Sashimi plots
(http://www.broadinstitute.org/igv/Sashimi)

IGV can overlay tracks.

Track overlay example

IGV can be used to combine tracks

IGV can be used to combine tracks

IGV can be used to combine tracks

IGVtools

• IGVTools can be used to post-process genomics data.
• Includes indexing, sorting and genome graph creation.

Where to get help?

• http://www.broadinstitute.org/igv/UserGuide

• https://groups.google.com/forum/#!forum/igv-help