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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
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- 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
- 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
Click an image from the start screen (red box).To choose a species and genome version
- Click a shortcut image (loads most recent genome)
or
- Choose
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- Species and Genome Version using the Current Genome tab
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- .
IGB start screen
If your species or genome
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version is not listed,
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Note |
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Depending on the genome, IGB may automatically load reference gene models from the IGB QuickLoad data server. |
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).
Select data sets you would like to view by
- checking the box (red arrow)
- click-dragging the data set into the Data Management table
When you remote data sources (Data Access tab) or by opening local files.
To open a data set , IGB adds it as new empty track to the main view and lists it in the Data Management table (orange arrows).
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The newly-added track is empty at first to give you more control over how much data are loaded into memory. |
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
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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 URL
When you open select a data sets or a file, IGB creates adds a new empty track and adds the file to the list of active data sets main view and lists it in the Data Management Table.
To load data into the main view, click Load Data.
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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
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view all at once
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, IGB does not
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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, load data into the viewer until you 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:
- 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).
- See also Searching in IGB
- Double click on a feature within the visual field to zoom to that feature (orange box/arrow).
- See also Selecting a feature
- 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).
- 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.
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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: