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- Whole 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)
- Whole Chromosome is the standard load mode for most file types. We generally recommend selecting Whole Chromosome, unless it is a very large file (e.g. CoolI1T1.bed, A_thaliana_Jun_2009.fa).
- Region in View 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 refresh the data to see the data within this region. This is easily accomplished if the reference genome for your species is already loaded (IGB automatically loads the reference sequences for most model organisms).
- Autoload is a new option in IGB6.5. This is an option for .bam 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 Autoload threshold (this is marked with a white arrow in the zoom bar; see below)red box). The Autoload zoom level can be adjusted to your needs. First, set the main view to the zoom level you want. Then, right click in any blank area of the view and select Set Autoload Threshold to Current View. This will change the needed zoom level AND will move the white arrow to indicate the new threshold setting. BE CAREFUL! If you set the Autoload threshold too high, IGB will try to load all of the indicated data, which could exceed the memory limit.
Refresh to Visualize
After the data are set to the appropriate Load Modes, simply Refresh to see the data. If you want all the tracks to display at once, use the Refresh button in the Data Access panel or the refrtesh icon at the top of the window. Alternatively, if you want to visualize one track at a time, use the individual refresh icon next to the tracks.
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