Fig. 3

Modeled SssI pulldown coverage, \(\sum \nolimits _{x \in i} \Lambda _{x}\), correlates with observed SssI pulldown coverage. Among 100 bp windows on chromosome 7 with at least 75% mappable bases, we calculate expected SssI Control window coverage, \(y_{i\Lambda } = \sum \nolimits _{x \in i} \Lambda _{x}\), from our model of pulldown alignments derived from previous MBD pulldown experiments. a A density plot shows that y_iΛ correlates with observed SssI pulldown coverage, y_iC, represented with offset 0.5 to allow for log-log plotting. b To account for parts of the genome that are less likely to be sequenced, we compare y_iΛ to y_iC/y_iI – wherever y_iI, the read coverage from the Input Control sample, is nonzero – which scales with the pulldown efficiency of genomic window i