IGB User's Guide
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  • Created by Unknown User (rhynwa), last modified on Jan 03, 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: Download and start IGB

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

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 your species and genome version, if available

When IGB first starts, you'll see the IGB start screen shown below.

  • Click an image or choose species and version under the Current Genome tab (blue box). 
    • For some species, gene models and cytological bands will automatically load.
  • If your genome of interest is not listed, don't choose anything and skip to Step 3.
IGB start screen

IGB after selecting the latest human genome. RefSeq alignments are show in blue.

Step 3. Load data sets from Data Source servers

Open a data source folder under the Data Sources and Data Sets file tree (red box). Select data sets you would like to view by

  • checking the box (red arrow)
  • click-dragging them into the Data Management table

When you select the data sets you would like to load, IGB will add new track to the main viewer and list the file in the Data Management table (orange arrows). Initially the track will be empty. This allows you to zoom in to a smaller region of interest before loading data into the memory.

To view data

  • Zoom or scroll to a region of interest
  • 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 adds new track to the main view (as a gray place holder 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.

Note: Many data files (especially BAM files) are huge and contain too much data to display at once. For this reason, IGB does NOT automatically load data from a newly opened file. To view data in a file, zoom and scroll to a region or gene of interest and click Load Data. IGB indicates regions that have not yet been loaded by displaying a slightly darker background color.

Reference Sequence

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 *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).
  • Double click on a feature within the visual field to zoom to that feature (orange box/arrow).
  • 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).

See also:

Step 6: Configure tracks

You can change track color, how IGB indicates strand, track labels, 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:

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