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IGB can create several useful graphs from annotation tracks. Although the Depth graph can be utilized for all annotations, the usefulness shines, in combination with the Mismatch graph, with .bam and other short read alignment files. Here, you can see how many reads are present at each nucleotide position (Depth) and where mismatches occur as compared to the genomic sequence file.
In IGB 7.0 we had added the benefit that after these graphs are created, they will dynamically update if you load more data into the parent tracks. Just move around and hit Load Data; the tracks will update and so will the IGB track.
Graph tracks, such as these, can be saved as .wig or .egr formatted files. Details about these formats can be found in File FormatsSee Saving and Sharing Data.
Depth Graph
You can generate an overview of the relative density of annotation coverage across an entire chromosome. The Make Annotation Depth Graph This feature dynamically graphs the number of annotations in a track that are present at each nucleotide across the genomic sequence. When you are completely zoomed in, and each pixel represents a single nucleotide base, the graph shows actual values for the number of reads aligned at that genomic location. Using the Select tool to hover over a particular point in the graph will open a tooltip with the actual number of reads at that point.
Right-click on the annotation in the label panel and choose Make Annotation Track Operations > Depth Graph.
The picture below shows a fully expanded .bam file, showing the difficulty of seeing any details. The second picture shows just the depth graph (.bam track is 'hidden') with the tool tip showing the number of reads aligned onto that specific genomic location.
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