Integrative Genomics Viewer

MRC Clinical Sciences 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

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