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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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 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. The RefGene has autoloaded.
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
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- 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
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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 (See Step 5) 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 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, and much more.
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