Introduction
Reference
As you get to know IGB, you'll find it offers many features designed to enrich your genome browsing experience.
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Here we provide a brief Quick Start Guide to help you get started using IGB.Bullet points link to pages that explain each topic.
Step 1:
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Download and start IGB
1. From the IGB homepage, go to Downloads or follow this link.
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Go to bioviz.org/igb and click Downloads.
- 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 Page - Small, medium, and large memory options
Step 2: Choose your species and genome version
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, if available
- Click an image or choose species and
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- version under the Current Genome tab (blue box).
- For some species, gene models and cytological bands will automatically load.
- If your genome of interest is not listed,
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- See the list of supported species in IGB.
- For most common model species, IGB will automatically load the reference gene annotations. For instance, if you selected Homo sapiens from the picture link, IGB would load and display the refseq annotations for H. sapiens February 2009.
- If the annotations do not automatically load, you can select the annotations you are interested in from the Data Sources file tree. Open the server folders to find don't choose anything and skip to Step 3.
IGB start screen
IGB after selecting the latest human genome. RefSeq alignments are show in blue.
Step 3. Load data sets from Data Source servers
- Select and load annotations
- Open data source folders under the Data Sources and Data Sets file tree (red box)
- Select data sets you would like to view by
- checking the box
- or click-dragging them into the Data Management table
When you select a data the data sets you would like to load
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, IGB will add new track (orange box) to the main viewer.
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To view data
- Zoom or scroll to a region of interest
- Click Load Data
- (green arrows
- , boxes) to
- load
- data into
- IGB
Step
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For every file opened in IGB, a place holder track is created, to show you where your data will appear when visualized. The data set/file will also appear in the Data Management Table. NOTE: IGB does not immediately display the contents of your file; bioinformatics data files often contain enormous amounts of data, more than any program can display. For example, a single short reads alignments ("BAM") file may contain millions of read alignments. IGB generally sets files to Load Region in View, which allows you to select the size of the region that you are going to load.
- Details about loading data
- IGB supported file formats
- Details on adding servers
- Creating Quickload sites
Drag-and-drop your file into IGB
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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
- Click-drag the file or Web link into the IGB main viewer
When you open a file, IGB adds new track to the main view.
Areas that are NOT loaded are grayed out (as you can see in the place holder tracks).
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: 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 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 a the reference sequence, use the File > Open Reference Sequence... option.
Choose from Data Sources and Data Sets folders
As shown above, you can easily navigate through the folders in the Data Sources and Data Sets sub panel. Simply click the tracks you are interested in loading.
Step
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5:
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Zoom in on a region of interest
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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, ie 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 Search tab and enter the name of a gene.
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- Double-click rows in the
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- results list to
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- jump to
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- a feature (red box/arrow).
- See also Searching in IGB
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- Double click on a feature within the visual field to zoom to that feature (orange box/arrow).
- See alsoSelecting a feature
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- Enter a coordinate range in the coordinate box and hit enter to zoom to that location (green box/arrow)
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- Click and drag within the coordinate axis to zoom to a region of interest (blue
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- box/arrow).
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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).
Step 5: Finish loading your data
Load the data for visualization from the Data Access tab either by using the Load Data button or the load icon for each individual track. Areas that are NOT loaded are grayed out (as you can see in the place holder tracks).
More about moving and zooming in IGB
1. Zooming. Use the sliders to zoom in or out on regions in IGB. To change the vertical zoom, use the vertical slider on to the left of data display window.
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See also:
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Step 6: Configure tracks
You can change track color, how IGB indicates strand, track labels, and much more.
To change track appearance
- Right-click (or control-click on Mac) a track label and choose Change or Configure.
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- . options
- Click File > Preferences
- Click a color swatch in the Data Management Table
See also: