Outline of Anchored ChromPET method. Details are in Materials and methods. (a) Y-primers containing the sequencing primer and the bar code (1, 2 or 3) ligated to sized genomic fragments. (b) RNA bait for anchoring the targeted region prepared by cloning the fragments in a TOPO-TA vector and in vitro transcription. (c) Y-primed library is selected on the RNA bait, eluted and amplified with paired-end primers to create the bar-coded libraries for paired-end sequencing. (d) Bioinformatics pipeline with sequence data.