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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.
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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 from the start screen menu (red box). These species will automatically load the current reference gene models.
- Choose species and version under the Current Genome tab (blue box). Some of these species will require you to select the reference gene models or another data file and load them (see Step 3)
- 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.
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Step 3.
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Open data sets from Available Data
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Open a data source folder under the Data Sources and Available 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 a data set, IGB adds it as new empty track to the main viewer and list the file view and lists it in the Data Management table (orange arrows). Initially the track will be empty
The track is empty at first. This allows you to zoom in to a smaller region of interest before loading data into the memory (see Step 5).To
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.
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When you open a file, IGB adds creates a 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:
| Note |
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Many data files |
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contain too much data to display at once. |
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For this reason, IGB does |
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not automatically load data from a newly opened file. To view data in a file, zoom |
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in and click Load Data. |
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Regions where data have not yet been loaded |
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have slightly darker |
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backgrounds. |
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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:
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- Use control+mouse wheel (Windows) or command+mouse wheel (Mac) to zoom in on the zoom stripe location (yellow box/arrow).
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
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