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IGB can create several useful graphs from annotation tracks. Although the Depth graph can be utilized The Depth Graph feature works for all annotations , the usefulness shines, but is most useful in combination with the a Mismatch graph Graph, with .bam and other short read alignment files. Here , you can 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).

In IGB 7.0 we had added the benefit that after 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 trackclick Load Data to load graphs for regions that have not yet been loaded.

Graph tracks , such as these, can may be saved as .wig formatted files.

Depth Graph

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(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 and choose Track Operations > Depth Graph (All).

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').

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