Fig. 4

Burrows-Wheeler Aligner allows efficient mapping of Hi-C reads both in the presence and in the absence of adapter sequences. For samples prepared using protocol Ma et al. (a), end-labelling was achieved by adapter ligation, whereas for samples prepared using protocol Ramani et al., biotin fill-in (b) DNA, we did not use any internal adapters. Reads were mapped by Hi-C pro [28] (bowtie2-based software) directly or, in the case of protocol Ma et al., after removing the adapter sequences (cutadapt split). Alternatively, reads were aligned using bwa without any pre-processing. Mapping efficiency is shown as a percentage of alignable reads (reported pairs). Each dot represents an independent Hi-C library preparation, and the significance of differences was computed using the Mann–Whitney test