IGB User's Guide
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  • Created by Unknown User (rhynwa), last modified on Jan 28, 2013
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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: Get and start IGB

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

2. Download and launch IGB.

If your computer has enough memory, we recommend the 2 or 5 GB option.

Step 2: Choose species and genome version

Click a start screen shortcut image (red box).

or

Choose Species and Genome Version using the Current Genome tab (blue box).

  • If your genome is not listed, skip to Step 3.

IGB start screen

Most species will automatically load the reference annotations

After IGB automatically loaded H. sapiens

Step 3. Choose data sets

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) by clicking on it.

Select data sets by

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

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
  • Drag the file or Web link into the IGB window

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

  • Zoom to a smaller region (See Step 5) if large data sets are selected
  • Click Load Data (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

To zoom in on a region of interest:

  • Use the zoom slider. Click in the main window for focus zooming (zoom stripe) and then drag the slider (purple box/arrow).
  • 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).
  • Double click a feature. (orange 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).

See also:

Step 6: Configure tracks

Select the Annotations tab, which 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:

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