When visualising large single scaffold genomes, it seems the HiC map is subsampled to decrease the size by a factor of 2.0. However, the genome position axes are not scaled. Although, the genome is ~2.4 Gbp, the map suggests that it is ~1.2 Gbp. Please see the attached image.
Moreover, the bed and bedpe tracks added to the map are also not aligned. When we scale track positions by a factor of 2.0, everything seems to align.
When visualising large single scaffold genomes, it seems the HiC map is subsampled to decrease the size by a factor of 2.0. However, the genome position axes are not scaled. Although, the genome is ~2.4 Gbp, the map suggests that it is ~1.2 Gbp. Please see the attached image.
Moreover, the bed and bedpe tracks added to the map are also not aligned. When we scale track positions by a factor of 2.0, everything seems to align.