Fig. 4

Simple viewpoint creation. (a) From the Analysis tab (Fig. 3) each individual viewpoint can be opened in a separate tab for visual inspection. The upper part displays tracks from UCSC’s genome browser and can be used for evaluation and orientation during editing of viewpoints. In this case, the selected digest is not well centered at the TSS. Detailed information about the digest that contains the TSS (marked with an asterisk) and the two adjacent digests are shown below. The indicated information about alignability, GC and repeat content refers to selected probes. Note that in this case the digests containing the TSS is unbalanced due to high GC content at the downstream margin. (b) The score for simple viewpoints is close to 1 for digests that are not too short and well centered at the TSS, whereas it is close to 0.5 if the TSS occurs at the outermost ends of digests. Such viewpoints can be easily identified by sorting the viewpoint table in the Analysis tab by score. (c) The user can select and deselect each individual digest. For the GATA1 viewpoint shown above, the adjacent downstream digest should be selected in order to center the viewpoint at the TSS