IGV Introduction

Overview

question Questions
objectives Objectives

time Time estimation: 2 hours

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

MainWindowIGV

Tool bar callout_1.jpg

Chromosome callout_2.jpg

Ruler callout_3.jpg

Tracks callout_4.jpg

Features callout_5.jpg

Track names callout_6.jpg

Attributes callout_7.jpg

File

Genomes

View

Tracks

Regions

Tools

GenomeSpace

Help

Tool Bar

Genome drop-down box icon_genome_dropdown

Chromosome drop-down box igv_chromdrop

Search box searchbox

Whole genome view icon_genome

icon_backforward

Refresh icon_refresh

Define a region icon_region_of_interest

icon_squish

icon_popuponoff

Zoom slider icon_zoom

Pop-up Menus

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

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

load_encode_RNA-seq_BAM

view_pairs

sashimi_plot

LOOKING AT ENCODE ChIP-Seq DATA

ChIP-Seq_bigwig

data_range

SOME OTHER THINGS YOU CAN DO

FOR IGV HELP AND DOCUMENTATION

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

congratulations Congratulations on successfully completing this tutorial!