HiCmaps
HiCmaps are standardized representations of chromatin interactions produced by Hi-C experiments. They capture the frequency with which pairs of genomic loci come into proximity in the three-dimensional nucleus, summarized as a two-dimensional contact map. A HiCmap is generated by sequencing crosslinked chromatin, mapping paired-end reads to a reference genome, assigning reads to genomic bins, and counting interactions between bin pairs. To reduce technical bias, HiCmaps are commonly normalized to correct for systematic effects such as distance-dependent decay, mappability, and fragment length, using methods like matrix balancing.
The resolution of a HiCmap depends on sequencing depth and bin size; finer resolutions (tens of kilobases)
Limitations of HiCmaps include sparse contact counts at high resolution, biases introduced during library preparation and