Principle of in silico simulations of ChIP-Seq tags mapping with gapped genome assemblies. In this example, the Xenopus scaffolds and the mouse chromosomes were concatenated in a random order and placed along each other. Each Xenopus assembly gap was then transposed onto the mouse genome, which was further sliced in order to reflect the fragmented nature of the Xenopus genome assembly. ChIP-Seq sequence reads were mapped with bowtie on the 'xenopized' mouse genome. Sequence reads mapping at multiple locations were discarded and peak calling was carried out with sissrs. The process is reiterated 20 times for statistical robustness. With ChIP-PET, the process is similar except that the two ends of each sequence read are mapped.