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The first step to loading data is to choose Species and Genome Version. IGB uses this information to offer data sources with relevant data sets. To set the species and version, select them in the Current Genome panel.
Alternatively, if you chose to open a file from File > Open File... or Open URL... the file selection widow will permit you to specify species and genome using the drop down menus at the bottom of the window.
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- Don't Load is the setting for not loading any data, but remaining in the Data Management Table
- Genome is primarily used with sequence files; this is the default load that IGB uses for the reference sequences for most model organisms (e.g. TAIR10 mRNA)
- Manual is the default Load Mode for IGB. This setting tells IGB to load only the region in view (e.g. CoolI1T1.sm.wig). For large files, such as .bam, .wig or other short read associated files, we strongly recommend that you zoom into a small region of interest, usually about <100Kb depending on your read density, and then Load Data to see this region. This is the default setting for most files.
- Auto is an option for BAM and SAM files (e.g. CoolI1T1.sm.bam), which will allow IGB to automatically load the data in view, if the view is zoomed below the Auto threshold (this is , marked with a yellow arrow in the zoom bar; red boxhead (red arrow). The Auto zoom level can be adjusted to your needs. First, set the main view to the zoom level you want. Then, View > Set AutoLoad Threshold to Current View. This will change the needed zoom level AND will move the yellow arrow to indicate the new threshold setting.
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If you set the Autoload threshold too high, IGB will try to load all of the indicated data, which could exceed the memory limit. |
Load Data to Visualize
After If the data is set to the appropriate Load Mode > Manual, simply click Load Data to visualize the data. If you want all the tracks to load data at once, use the Load Data button (red box, arrow); to load a single track use the Load Data icon in the Data Management Table (red arrow). Sequence can be loaded from the Load Sequence button (purple box, arrow). 
You might partially load a track and then zoom out to show a greater region of the data sets. IGB will show gray where the track is not loaded yet .
(red arrows). 