In this vignette we present a somewhat contrived ChIP-seq study - contrived in that it is not organized around an actual research problem. Instead, this vignette demonstrates methods you would likely use to do visual QC and exploratory data analysis a ChIP-seq experiment.
We begin with ENCODE data of CTCF binding on chromosome 3, on the hg19 reference genome, in the vicinity of the GATA2 gene. We will
The two images below illustrate the final state of igv in your browser at the conclusion of the code found below. The first view spans 35kb:
The second spans less than 1200 bases.