Creating Graphs
IGB creates these graphs from a selected track. Although the first two graphs (Coverage and Depth) can be utilized for all annotations, their usefulness shines, in combination with the third graph (Mismatch) with .bam and other short read alignment files. Here, you can see where reads are (Coverage), how many reads are present (depth graph) and where mismatches occur as compared to a sequence file.
Coverage Graph
Depth Graph
You can generate an overview of the relative density of annotation coverage across an entire chromosome. The Make Annotation Coverage Track feature dynamically graphs the relative number of annotations in a track that are present at each pixel across the main window. As you zoom in and each pixel represents a smaller number of nucleotides, the graph automatically adjusts to indicate the relative number of annotations present in the smaller region covered by that pixel. When you are completely zoomed in, and each pixel represents a single nucleotide base, the graph shows either a 0 (no annotation is present) or a 1 (an annotation is present) for each pixel.
To show the density of annotation coverage for an annotation type that you are viewing:
- Right-click on the annotation type in the Tracks panel and choose Make Annotation Coverage Track.
The following illustration shows the relative annotation coverage at each pixel when the view is zoomed all the way out. In this example, suppose you conclude that the density of the circled region is significant and you want to examine it more closely.
After you zoom in to display the relative annotation density within the region that is circled in the illustration above, you might decide to look more closely at the region of greater annotation density at the end of the pictured region.