Basically, the R-loop zone detected independently by multiple technologies in multiple cells, and associated with specific genomic features, more likely represents a bona fide R-loop zone (see also Q5 and Q6). R-loopBase provides three different ways for evaluation of a given R-loop zone.
(1) Each R-loop zone belongs to one of nine levels (levels 1-9). The higher the level is, the more technologies it was detected by and the more reliable the R-loop zone is expected to be.
(2) Each R-loop zone is further coded with colored box to indicate which sub-region is detected in which cells and by which technology (Peak Detail column). The genomic coordinates of a given colored box will be shown by hovering the mouse on top of the colored box. This will allow you to locate the core regions with multiple independent evidences.
(3) It is well known that R-loops are associated with multiple genomic features, such as high GC-skew, G4 formation and single-strand DNA exposure. By clicking the coordinate of a given R-loop zone on R-loop page, you will be directed to Browser to visualize each R-loop zone in the context of all above genomic features, which allows you to make your own judgement on whether the R-loop zone is reliable.
