Figure 2.

Splicing summary with coordinate truncate gaps. An example of a plot made from multiple tracks. At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The middle track shows the slicing summary plots for the gene ALDOA for normal and tumor samples. Splicing is shown as arches and size is used to represent junction counts and color represents novelty: blue indicates known splicing events against the model and red indicates novel splicing events. The height of arches is proportional to the distance between the two ends of the arches, or the distance between the junction reads. Coverage is shown by position to address supporting evidence in the raw data. The splicing summary plots are aligned with a view of the gene structure in the bottom track. The thicker rectangle represents the Consensus Coding DNA Sequence (CCDS) transcripts. The plots in both tracks are made with truncate gaps coordinate transformation. The space dedicated to introns has been significantly reduced, and the exonic regions are shown in detail, even though the entire gene region is in view.

Yin et al. Genome Biology 2012 13:R77   doi:10.1186/gb-2012-13-8-r77
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