There are huge differences in where R-loops are located within the human genome depending on which R-loop mapping technology is used. Considering that misleading conclusions will be drawn if R-loops are mis-assigned, it is thus of the highest priority to define a human R-loop map for the R-loop research community. Currently, it is premature to conclude which technology is superior to others with regard to precise mapping of R-loops. However, it is plausible that R-loop peaks supported by multiple technologies are more likely bona fide R-loops.

Following this principle, we performed integrative analysis of all mapped R-loop peaks in control cells identified by all technologies. First, stranded R-loop peaks were merged as R-loop zones on Watson or Crick strand separately. Non-stranded R-loops, if overlapped with stranded R-loop peaks, were also assigned to Watson or Crick R-loop zones accordingly. The remaining non-stranded R-loop peaks were merged as non-stranded R-loop zones. Second, the resulting R-loop zones were further partitioned into sub-regions of n different confidence levels, where n is the minimal number of technologies they were detected by. For example, R-loop zones of level 3 were those co-detected by >=3 technologies. The higher the level is, the more conservative the R-loop zones are.