Introduction
As you get to know IGB, you'll find it offers many features designed to enrich your genome browsing experience.
However, most of us want to 'jump right and make it work' and don't need to explore these many features right away.
Here we provide a brief Quick Start Guide to help you get started using IGB.
Bulletpoints link to pages that explain each topic.
Choose your IGB
1. From the IGB homepage, go to Downloads or follow this link.
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.
Choose your species and genome version
1. IGB opens to with the Data Access tab open. Choose Species and Genome Version. If your genome of interest is not listed, leave it set to 'Unknown Species' and 'Unknown genome.'
- See the list of supported species in IGB.
2. Depending on the genome, IGB will next load reference gene model annotations into the display.
3. Open the server folders listed in Data Sources and select additional data sets you would like to load. Click the Refresh Data button to load the data into the view.
Loading your own data files
Drag-and-drop your file into IGB
1. Drag and drop the file from a Web link or from your computer desktop. You can also access files using File > Open File... or File > Open URL... If you are dragging/opening a file from a private server, you may need to log in to access the data. If so, IGB will open a window for you to enter a user name and password.
- Details about loading data.
- IGB supported file formats.
- Details on adding servers
- Creating Quickload sites.
2. IGB WILL NOT IMMEDIATELY DISPLAY DATA FROM 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 uses Load Mode settings to give you total control over how much data get displayed at once.
Once you've added a file to IGB, it will appear in the Load Mode table in the Data Access Panel.
Select a Load Mode option from the Choose Load Mode for Data Sets list.
For larger files, such as BAM or wig (bedGraph) files, choose Region in View.
Choose Whole Genome for annotation data sets with fewer than 200,000 genes. Then click the Refresh Data button to trigger loading of data into the main IGB display.
Load data in a region of interest (Zooming in)
1. If you're working with large files, you should zoom in to a smaller area before loading your data. To zoom in on a region of interest, you can:
- Click the Search tab and enter the name of a gene. Click rows in the returned list to zoom to that feature (red box/arrow).
- Double click on a feature within the visual field to zoom to that feature (orange box/arrow).
- 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 the zoom slider bar to zoom down to the gene model level (purple box/arrow).
- Use control+mouse wheel (Windows) or command+mouse wheel (Mac) to zoom in on the zoom stripe location (yellow box/arrow).
2. Load the data for visualization from the Data Access tab either by using the Refresh Data button or the refresh icon for each individual track. Areas that are NOT loaded are grayed out.
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.
2. Pan left or right, up or down. Use the horizontal or vertical scrollbars to move left and right or up and down. Click-drag the arrow tool to pan left or right. Drag the hand (grab) tool left or right to adjust the display.
Note: At any time, you can hide or show the right, left or bottom trays, as well as increase the main viewing field. Adjust the size of the IGB window to get a layout you like.