Finally, read pairs with at least one allele specific mate are used to construct allele specific contact maps.
In allele-specific mode, the .validPairs files will contain an additional columns with the allele status of each reads pair. Therefore, valid pairs assigned to ‘G1-G1’, ‘G1-UA’ or ‘UA-G1’ are used to build the G1 genome-wide contact maps. In the same way, ‘G2-G2’, ‘G2-UA’, ‘UA-G2’ pairs will be used to generate the G2 genome-wide contact maps.
All maps are then normalized using the ICE method.