Figure 2: Example of manual scaffold editing based on linkage map information
Example of manual repositioning of regions of the scaffolds from the Hi-C step using information from the linkage map and male versus female dot-plots. (A) ALLMAPS graphs for a male Hi-C scaffold showing position of markers derived from male (orange) and female (green) mapping population samples. Sections with crossing marker positions (left subgraph) and negative slope (right subgraph) indicate regions in the scaffold with orientation inconsistent with the linkage map. Sections in right subgraph that are parallel but not collinear with the trend of the curve indicate regions in the scaffold with ordering inconsistent with the linkage map; (B) ALLMAPS graphs for a female Hi-C scaffold showing position of markers derived from male and female mapping population samples; (C) Dot-plot (mummerplot with data generated by NUCmer) of the male and female Hi-C scaffolds. Blue arrows indicate the position and orientation of the Chicago scaffolds that were inconsistent with linkage map information. Black arrows indicate positional reordering of these scaffolds, and red arrows indicate a flip of the scaffold; (D) ALLMAPS graphs for the same male Hi-C scaffold after manual repositioning showing consistency with the linkage map information; (E) ALLMAPS graphs for the same female Hi-C scaffold after manual repositioning, showing consistency with the linkage map information; (F) Dot-plot of the male and female Hi-C scaffolds after manual repositioning, showing consistency between sexes. Blue arrows demark the position and orientation of the Chicago HiRise scaffolds after the manual repositioning.