Using the Integrative Genomics Viewer

Bioinformatics Galaxy Course

MPI-IE & University of Freiburg

To start IGV, go to the IGV downloads page: https://www.broadinstitute.org/software/igv/download.

User Interface

Main Window

Tool bar

• The tool bar provides access to commonly used functions. The menu bar and pop-up menus (not shown) provide access to all other functions.

Chromosome

• The red box on the chromosome ideogram indicates which portion of the chromosome is displayed. When zoomed out to display the full chromosome, the red box disappears from the ideogram.

Ruler

• The ruler reflects the visible portion of the chromosome. The tick marks indicate chromosome locations. The span lists the number of bases currently displayed.

Tracks

• IGV displays data in horizontal rows called tracks. Typically, each track represents one sample or experiment. This example shows methylation, gene expression, copy number and mutation data.

Features

• IGV also displays features, such as genes, in tracks. By default, IGV displays data in one panel and features in another, as shown here. Drag-and-drop a track name to move a track from one panel to another. Combine data and feature panels by selecting that option on the General tab of the Preferences window.

Track names

• Track names are listed in the far left panel. Legibility of the names depends on the height of the tracks; i.e., the smaller the track the less legible the name.

Attributes

• Attribute names are listed at the top of the attribute panel. Colored blocks represent attribute values, where each unique value is assigned a unique color. Hover over a colored block to see the attribute value. Click an attribute name to sort tracks based on that attribute value.

Menu Bar

File

• Load from File - Displays genomic data from one or more files.

• Load from URL - Displays genomic data from a file identified by URL.

• Load from Server - Displays genomic data from the IGV data server.

• Load from DAS - Displays genomic data from a Distributed Annotation Server (DAS)

• New Session - Unloads all currently loaded data, as if you exited and restarted IGV

• Open Session - Opens a previously saved session file.

• Save Session - Saves your current settings to a named session file

• Save Image - Saves a snapshot of the IGV window to a graphics file, omitting the menu bar and tool bar. Can save in .png, .jpg, or .svg format.

• Exit - Closes IGV.

Genomes

• Load Genome from File - Loads a genome into IGV from your file system.

• Load Genome from URL - Loads a genome into IGV from a web URL.

• Load Genome from Server - Loads a genome into IGV from the IGV data server.

• Create .genome File - Save your genome file in .genome format.

• Manage Genome List - Choose which genomes to display in the genome drop-down menu in the tool bar.

View

• Preferences - Opens a tabbed menu of data display preferences.

• Color Legends - Displays color legends for track data, which may be modified.

• Show Name Panel - Shows/hides the track name panel.

• Set Name Panel Width - Resets the track name panel width.

• Show Attribute Display - Shows/hides attributes and attribute values.

• Select Attributes to Show - Shows/hides selected attributes and attribute values.

• Show Header Panel - Shows/hides the chromosome location header panel.

• Reorder Panels - Allows the user to reorder the display panels.

• Go to - View and select loci visited in your navigation history.

Tracks

• Sort Tracks - Sorts track data.

• Group Tracks - Groups track data.

• Filter Tracks - Filters track data.

• Fit Data to Window - Sets the track height to display all of the data, or as much data as possible.

• Set Track Height - Sets the track height to a specified value.

Regions

• Region Navigator - Opens the region navigator.

• Gene Lists - Opens the gene lists window.

• Export Regions - Saves currently defined regions of interest to a BED file. If no regions of interest are defined, no BED file is created.

• Import Regions - Imports regions of interest from a BED file.

Tools

• Run Batch Script - Executes a series of sequential tasks. Users can load at .txt file that contains a list of commands, one per line, that will be run by IGV. The accepted commands are the same as the IGV Port Commands.

• Run igvtools - Launches the igvtools interface window.

• Find Motif - Search for a particular nucleotide sequence in the reference genome.

• Gitools Heatmaps - Data and results are represented as browsable heatmaps. Data can be exported from IGV in gitools format, or loaded directly into a running gitools session. See http://www.gitools.org for details.

• BEDTools - A fast, flexible suite of tools used to compare sets of genomic features. IGV uses BEDTools to compare features in loaded tracks, and view the results as a new track.

GenomeSpace

• Load File from GenomeSpace - Load a file into IGV from your GenomeSpace directory.

• Load Genome from GenomeSpace - Load a genome into IGV from your GenomeSpace directory.

• Save Session to GenomeSpace - Save current IGV session to your GenomeSpace directory.

• Load Session from GenomeSpace - Load a previous session from your GenomeSpace directory.

• Logout - Log out of GenomeSpace

• Register - Register a new account at GenomeSpace

Help

• User Guide… - Displays the IGV User Guide.

• Help Forum… - In your default web browser, opens the home page for the igv-help forum.

• About IGV - Displays IGV version and build number.

Tool Bar

Genome drop-down box

• Loads a genome.

Chromosome drop-down box

• Zooms to a chromosome.

Search box

• Displays the chromosome location being shown. To scroll to a different location, enter the gene name, locus, or track name and click Go.

Whole genome view

• Zooms to whole genome view.

• Moves backward and forward through views of the genome like the back and forward buttons in a web browser.

Refresh

• Refreshes the display.

Define a region

• Defines a region of interest on the chromosome.

• Reduces the row height on all tracks to fit all data for the region in view into the window; will also expand tracks (to their maximum preferred size) to fill the view, if needed.

• Toggles the pop-up information windows in IGV on or off.

Zoom slider

• Zooms in and out on a chromosome.

Pop-up Menus

To select tracks and display the pop-up menu, do one of the following:

• Right-click a track to select it and display the pop-up menu.

• Right-click an attribute value to select all tracks with that attribute value and display the pop-up menu. Tip: Keep in mind that right-clicking an attribute may select tracks that are not visible in the data panel. Scroll down the data panel to view all the selected tracks.

• Control-click track names (Mac: Command-click) to select the tracks, then right-click one of the selections to display the pop-up menu.

Commands in the track pop-up menu change the display options for the selected tracks. Most changes made via the pop-up menu are lost when you exit IGV unless you save the session. In a few cases, changing the pop-up menu also changes an option in the Preferences window; these changes are persistent.

Using IGV: Examples

LOOKING AT ENCODE RNA-SEQ DATA

• Open IGV (.igv.sh from command line)

• Load the human genome : In the toolbar, Click Genome > Load Genome from Server > Search and select Human (hg19)

• Load the encode RNA-Seq BAM files: Go to File > Load from ENCODE > Select C2C12 RNA-Seq BAM files (See image in the Pdf)

• Go to your favorite location in the genome by entering the location in the Search box, zoom in to the reads by using Zoom button.

• You can change the track properties by right-click on the track. Select View as pairs to see the left and right pairs of paired-end reads.

• You can make a sashimi plot to see reads aligning to each junction. Right-click > Sashimi plot.

• Save what you see by going to File > Save Image.

LOOKING AT ENCODE ChIP-Seq DATA

• Go to File > Load from ENCODE > Select C2C12 ChIP-Seq bigwig files

• Reset the track heights to make them comparable. Right click on the track > Set data range. Then change the scale.

• You can also change the track colors, name and chart type (line,bar,heatmap).

• Save the image (File > Save Image)

POPULAR FILE FORMATS THAT YOU CAN LOAD IN TO IGV

• BAM

• BED

• BedGraph

• bigBed

• bigwig

• FASTA

• GFF/GTF

• MAF

• SAM/BAM

• VCF

• PSL

• Narrowpeak

• Many more

SOME OTHER THINGS YOU CAN DO

• Take multiple images from regions in a bed file. First make a batch file from the bed file using bedtools (bedtoIgv). Then load the script in Tools > Run Batch Script.

• Find a given motif. Tools > Find Motif.

• Set startup preferences. View > preferences.

• For more, have a look at the IGV documentation.

FOR IGV HELP AND DOCUMENTATION

GOTO: https://www.broadinstitute.org/igv/ or Click on Help in IGV menu.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

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Citing this Tutorial

1. Anton Nekrutenko, Joachim Wolff, Anne Pajon, IGV Introduction (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/igv-introduction/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{introduction-igv-introduction,
author = "Anton Nekrutenko and Joachim Wolff and Anne Pajon",
	title = "IGV Introduction (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/introduction/tutorials/igv-introduction/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

t{ hist[0] | to_stars }}	1
t{ hist[0] | to_stars }}	2
t{ hist[0] | to_stars }}	1
t{ hist[0] | to_stars }}	1
t{ hist[0] | to_stars }}	6

June 2023

• 1 stars: Disliked: there is no analysis of cases, it does not really help a lot to use the IGV, it is needed more options to move, colors etc

July 2022

• 1 stars: Liked: more detailed form example was not explained clearly

January 2022

• 1 stars: Liked: nothing Disliked: Does not tell me how to get FreeBayes data from Galaxy into IGV. IGV states that it cannot recognize the file. I have used these programs before, but something is different now.

May 2021

• 2 stars: Disliked: It is not clear which files to choose, because "C2C12" clearly isnt available.

February 2020

• 4 stars: Liked: It is easy to follow and summurazing many tools features as much as possible. Disliked: A real-life and frequently performed case tutorial could be shown for demonstrating what could be done in IGV.

August 2019

• 1 stars: Disliked: RNASeq of C2C12 not available

February 2019

• 3 stars: Disliked: Cannot find C2C12 file

January 2019

• 1 stars: Disliked: Actually show some use-cases (there is only one and i am unable to load ENCODE data)