Mapping of a read pair to a reference genome containing a repetitive sequence. Mapping of a read pair to a reference genome. The first read of the pair maps to a unique location, the second read maps to a repetitive sequence, present in two copies in the genome. The read may therefore be assigned to two locations. The method used by the Dekker group considers that these two locations are equiprobable, whereas the first location should be preferred. This results in an overestimation of the interaction frequency between distant loci when at least one of the involved loci contains a repetitive sequence.
Véron et al. BMC Genomics 2011 12:303 doi:10.1186/1471-2164-12-303