Similarity and Differences of HMRs and PMDs from H1 and IMR90

In this section, we wish to prepare files that record the amount of similarity and differences of HMRs (and also PMDs) between the two cell lines (i.e. H1 and IMR90). There may be several ways to do this depending on what information you wish to present to your audience. Below, we showed you one such method.

The concept is that we use cat command to join the HMRs or PMDs from H1 and IMR90, coordinate-sorted the data with sortBed and merge any overlapping regions with mergeBed. Common regions between H1 and IMR90 will be merged to become a wider region in this process. Then, we pass these merged HMRs into two consecutive intersectBed commands to identify the number and amount of overlaps between merged HMRs and HMRs in H1 (as well as that in IMR90).