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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:
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Get and start IGB
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- Go to
...
...
- and click
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- Go to IGB Download Page
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
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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 (loads most recent genome)
or
- Choose
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- Species and
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- 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
IGB after selecting the human genome
you can view it if you have a fasta or 2bit file with sequence data. See Custom Genomes
Step 3. Open data sets
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Open data sets from
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Open a folder under the Available Data file tree (red box) by clicking on it.
Select data sets you would like to view by
- checking the box (red arrow)
- click-dragging the data set into the Data Management table
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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...
- Enter file name or URL
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
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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.
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 enter a URL
- Click-drag the file or Web link into the IGB main viewer
To load data into the main view, click Load Data.
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Many data files and data sets (such as BAM files) contain too much data to display at once. For this reason, IGB gives you total control over when and how data are loaded. To load and view data, zoom in on a region and click the Load Data button. Regions where data have not yet been loaded have slightly darker backgrounds. |
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. The sequence data will appear below the Coordinate Axis in the center of the display.
Step 5: Zooming 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.
To zoom in on a region of interest:
- Use the zoom slider. Click in the main window to focus zooming and then drag the slider to the right.
- 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).
- See also Searching in IGB
- Double click a feature to zoom in on it (orange box/arrow).
- See also Selecting a feature
- Enter coordinates in the coordinate box and hit enter to zoom to that location (green box/arrow)
- Click-drag coordinate axix to zoom in on a region of interest (blue box/arrow).
- Keyboard shortcuts Use control+mouse wheel (Windows) or command+mouse wheel (Mac) to zoom in on the zoom stripe location (yellow box/arrow).
See also:
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. 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 color, how IGB indicates strand, track labels, track label color and font, click the track label and use the Annotation or Graph tab to change to change color, track height, annotation stack height, and much more.
To change track appearance
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label, amount of data shown
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(stack height), and other options.
See also: