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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 use this Quick Start Guide will help you get started using IGB.
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Step 1: Get and start IGB
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- Go to
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- and click
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- Go to IGB Download Page
2. Download and launch IGB.
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- the Download button
- Select and download the installer for your platform
If you have trouble starting IGB, visit the help page on BioViz.org for assistance.
Step 2: Choose species and genome version
To choose a species and genome version
- Click a
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- shortcut image (
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- loads most recent genome)
or
- Choose Species and Genome Version using the Current Genome tab
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- .
IGB start screen
If your species or genome version is not listed,
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IGB start screen
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Most species will automatically load the reference annotations |
After IGB automatically loaded H. sapiens
you can view it if you have a fasta or 2bit file with sequence data. See Custom Genomes
Step 3.
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Open data sets
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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 into memory. |
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
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Open data sets from remote data sources (Data Access tab) or by opening local files.
To open a data set from an IGB Quickload data source (see About IGB Quickload)
- Select Data Access
- Select data sets in the Available Data section
To open local files on your computer
- Select File > Open File... or File > Open URL...
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- Enter file name or
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- URL
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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).
- See also Selecting a feature
- 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 Zooming
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
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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When you select a data sets or a file, IGB adds a new empty track to the main view and lists it in the Data Management table. Empty regions in the new track that do not have data loaded are gray.
IGB window after opening human genome RNA-Seq coverage graphs from Adrenal Gland, Kidney, and Thymus data sets
Step 4: Zoom in
Because many data files contain too much data to view all at once, IGB does not load data into the viewer until you click the Load Data button.
Before loading data, zoom in to a region.
- Click a location in the main view
- Drag the horizontal zoom slider or use plus and minus buttons
IGB horizontal zooming controls
Other ways to zoom
Other ways to zoom include
- Search for a gene by name or keyword (For example, TBATA or thymus)
- Double-click an exon or gene model to zoom in on it
- Click-drag the coordinate axis to zoom in on a region
See also:
Step 5: Load data
To load data, click Load Data button. Regions with loaded data show the selected background color; areas without loaded data appear darker.
IGB after loading data
See also:
Step 6: Configure tracks
You can reorder the tracks by dragging the Track Label (the Data Management Table reflect changes).
To change style elements of a track, click the track label and use the Annotation or Graph tab to change to change color, track height, annotation label, amount of data shown (stack height), and other options.
See also: