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 Quick Start Guide will help you get started using IGB.

Step 1: Download and start IGB

1. Go to bioviz.org/igb and click Downloads.

Go to IGB Download Page

2. Click the IGB image to download and launch IGB. If your computer has enough memory, we recommend choosing the high memory (2 or 5 GB) option.

IGB Download - Small, medium, and large memory options

Step 2: Choose species and genome version

Click a start screen (red box) shortcut image.

or

Choose species and genome version using the Current Genome tab (blue box) menus.

If your genome of interest is not listed, don't choose anything and skip to Step 4.

IGB start screen

IGB after selecting the human genome

Step 3. Open data sets and click Load Data

Choose data sets from Available Data file tree

Open a folder under the Available Data file tree (red box) by clicking on it.

Select data sets you would like to view by

checking the box (red arrow)
click-dragging the data set into the Data Management table

When you open a data set, IGB adds it as new empty track to the main view and lists it in the Data Management table.
The newly-added track is empty at first to give you more control over how much data are loaded into memory. (orange arrows)

Click Load Data button to view data

Zoom or scroll to a region of interest (See Step 5) then
Click Load Data (green arrow, box in above image) to load data into the IGB main view.

Step 4: Load data from local files

To view data from local or remote files

Use File > Open... or File > Open URL... to select a file or enter a URL
Click-drag the file or Web link into the IGB main viewer

To load data into the main view, click Load Data.

Many data files and data sets (such as BAM files) contain too much data to display at once. For this reason, IGB gives you total control over when and how data are loaded. To load and view data, zoom in on a region and click the Load Data button. Regions where data have not yet been loaded have slightly darker backgrounds.

Loading a reference sequence (optional)

If you have a sequence file (fasta, 2bit, bnib, etc.) that you would like to use as the reference sequence, use the File > Open Reference Sequence... option. After selecting the file, click the Load Data button to load sequence. The sequence data will appear below the Coordinate Axis in the center of the display.

Step 5: Zooming in on a region of interest

If you're working with large files such as .bam, .sam, .wig, .bedGraph, you should 'zoom in' to a smaller area before loading your data.

To zoom in on a region of interest:

Use the zoom slider. Click in the main window to focus zooming and then drag the slider to the right.
Search for a gene. Click the Advanced Search tab and enter the name of a gene. Double-click rows in the results list to jump to a feature (red box/arrow).
- See also Searching in IGB
Double click a feature to zoom in on it (orange box/arrow).
- See also Selecting a feature
Enter coordinates in the coordinate box and hit enter to zoom to that location (green box/arrow)
Click-drag coordinate axix to zoom in on a region of interest (blue box/arrow).
Keyboard shortcuts Use control+mouse wheel (Windows) or command+mouse wheel (Mac) to zoom in on the zoom stripe location (yellow box/arrow).
- See also Zooming

Step 6: Configure tracks

You can change track color, how IGB indicates strand, track labels, track label color and font, track height, annotation stack height, and much more.

To change track appearance

Open the Annotations panel. This panel allows you to change style, size of the tracks, amount of data shown within the track, as well as offers various functions that can be performed on the track.

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Quick Start