Q: Is it possible to retrieve all methylation states for a set of tissues regardless its values
A: Yes, in the section “Retrieve unmethylated contexts” the user can choose a methylation threshold of 1. This means that all cytosine contexts for which information in all tissues exist will be written out.
Q: What does the column “strandDiff” in the dump download files mean?
A: This is the absolute difference between the methylation levels in both strands. Thus, this column can be used to detect hemimethylated positions. If for one strand no data exists (i.e. not a single read mapped), than the value is set to -1 (missing value).