IGB User's Guide
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Table of Contents

Introduction

As you learn to use IGB, you'll find it offers many features that make it one of the best tools available for visualization and exploration of genomic data sets.

If you are new to IGB, the following six step use this Quick Start Guide will help you get started using IGB.

Table of Contents

Step 1: Get and start IGB

...

...

  • and click the Download button
  • Select and download the installer for your platform

If you have trouble starting IGB,   see visit the Troubleshooting page or feel free tocontact us. help page on BioViz.org for assistance. 

Step 2: Choose species and genome version

There are many To choose a species and genome versions in IGB. You can:version

  • Click a start screen shortcut image .
Info

These species will automatically load the most current reference annotations

IGB showing the H. sapiens RefGene models

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  • (loads most recent genome)

or

  • Choose Species and Genome Version using the Current Genome tab.

...

IGB start screen
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If your species or genome version is not listed,

...

you can view it if you have a fasta or 2bit file with sequence data. See Custom Genomes

Step 3.

...

Open data sets

Info

When you select a file, IGB adds a new empty track to the main view and lists it in the Data Management table. Since many data files and data sets (such as BAM files) contain too much data to display all at once, you will control how much data are loaded.

Available Data folders

Open a folder under the Available Data file tree (red box) and select data sets:

  • Check the box (red arrow)
  • Drag the data set into the Data Management table

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Local files

To view data from local or remote files

...

Open data sets from remote data sources (Data Access tab) or by opening local files.

To open a data set from an IGB Quickload data source (see About IGB Quickload) 

  1. Select Data Access
  2. Select data sets in the Available Data section

To open local files on your computer

  1. Select File > Open File... or File > Open URL...

...

  2. Enter file name or

...

  1. URL

...

Reference sequence

If you have a reference sequence in the fasta, 2bit, or bnib format, File > Open Reference Sequence... will put the sequence in the Coordinate Axis in the center of the display (after Load Data button is used).

Step 4: Click Load Data button

  • If large data sets are selected, zoom to a smaller region (See Step 5)
  • Click Load Data button (green arrow, box in above image).

This will load and draw the data and sequences that you have selected in the Main View.

Step 5: Zoom in

  • Use the zoom slider. (purple box/arrow).
  • Search for a gene. Use the Advanced Search tab, double-click result to jump to a feature (red box/arrow).
  • Enter coordinates in the range box. (green box/arrow).
  • Click-drag within the coordinate axis. (blue box/arrow).
  • Use keyboard shortcuts. Use control+mouse wheel (Windows) or command+mouse wheel (Mac) (yellow box/arrow).

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See also:

...

When you select a data sets or a file, IGB adds a new empty track to the main view and lists it in the Data Management table. Empty regions in the new track that do not have data loaded are gray.

IGB window after opening human genome RNA-Seq coverage graphs from Adrenal Gland, Kidney, and Thymus data sets
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Step 4: Zoom in

Because many data files contain too much data to view all at once, IGB does not load data into the viewer until you click the Load Data button.

Before loading data, zoom in to a region.

  1. Click a location in the main view
  2. Drag the horizontal zoom slider or use plus and minus buttons

IGB horizontal zooming controls
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Other ways to zoom

Other ways to zoom include

  • Search for a gene by name or keyword (For example, TBATA or thymus)
  • Double-click an exon or gene model to zoom in on it
  • Click-drag the coordinate axis to zoom in on a region

See also:

Step 5: Load data

To load data, click Load Data button. Regions with loaded data show the selected background color; areas without loaded data appear darker.

IGB after loading data
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See also:

Step 6: Configure tracks

You can reorder the tracks by dragging the Track Label into the position you want (the Data Management Table reflect changes).

The Annotations tab will allow you To change style elements of a track, click the track label and use the Annotation or Graph tab to change to change color, sizetrack height, annotation label, amount of data shown as well as other various functions(stack height), and other options.

See also: