Fig. 6

Extended viewpoints. The extended approach is intended for in-depth analysis of a few hundred predefined genes of interest. (a) Instead of restricting the view only to digests containing the TSS, minimal distances to the TSS in up and downstream directions can be specified by the user. All digests that overlap the this range and satisfy the design parameters are selected. (b) Extended viewpoint for GATA1. The Copy URL button of the Viewpoint editor tab can be used to visualize viewpoints in UCSC’s genome browser. Just as for the embedded view within GOPHER, selected digests are indicated by colored boxes in the background. This representation has the advantage that additional custom tracks can be loaded in order to evaluate viewpoints. In this case the track for alignability is displayed (green). For this track, the alignability is standardized to values greater or equal 0 and lower or equal 1. For example, a value of 1/2 means that the corresponding k-mer occurs 2 times in the genome. The unbalanced digest at the TSS is not selected but can selected manually or directly during creation of viewpoints, if Unbalanced margins is set