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IGB can create several useful graphs. can be created by right-clicking on a track's label and highlighting Track Operations. A list of graphs and other track operations compatible with the track are displayed and may be selected to create a child track. The track operations that create graphs are:
- Depth Graph (All)
- Depth Graph (Start)
- Mismatch Graph
- Mismatch Pileup Graph
After these graphs are created, click Load Data to load graphs for regions that have not yet been loaded. Graph tracks may be saved as .wig formatted files.
The Depth Graph feature works for all annotations but is most useful in combination with a Mismatch Graph, with .bam and other short read alignment files. Here you can . This allows you to see how many reads are present at each nucleotide position (Depth Graph) and where mismatches occur as compared to the genomic sequence file (Mismatch Graph).
After these graphs are created, click Load Data to load graphs for regions that have not yet been loaded.
Graph tracks may be saved as .wig formatted files.
Depth Graph (All)
Depth Graph (All) allows you to generate an overview of the relative density of annotation coverage across an entire chromosome (this is also known as a coverage 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 track's label and choose Track Operations > Depth Graph (All).