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 an image from the start screen (red box).

or

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

• 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 or files and then click Load Data

Choose data sets from Available Data file tree

Open a folder under the Available Data file tree (red box).

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 (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) 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
• Click-drag the file or Web link into the IGB main viewer

When you open a file, IGB creates a new empty track and adds the file to the list of active data sets in the Data Management Table.

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

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 into the Coordinate Axis.

Step 5: Zoom 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, i.e. select a smaller region of data to load. To zoom in on a region of interest, you can:

• Use the zoom slider to zoom in on a gene (purple box/arrow). Click in the main window to focus zooming and then drag the slider to right to zoom in.

• 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 on a feature within the visual field to zoom to that feature (orange box/arrow).
  • See also Selecting a feature

• Enter a coordinate range in the coordinate box and hit enter to zoom to that location (green box/arrow)

• Click and drag within the coordinate axis to zoom to a region of interest (blue box/arrow).

• Use control+mouse wheel (Windows) or command+mouse wheel (Mac) to zoom in on the zoom stripe location (yellow box/arrow).
  • See also Detailed use of the zoom function and the zoom stripe

See also:

• More about scrolling/panning in IGB
• More about the main view
• More about the tabbed panels and about customizing them.

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.

See also:

• More about customizing the style of tracks.
• Preferences