I am currently working with WGBS methylation data from TCGA. It appears that these bed files have been generated using the tool BisSNP and contain the chromosome name, start coordinate, end coordinate, methylation value in percent, the coverage, the strand etc. According to the information of the package RnBeads, the coordinates are 0-based, spanning the first and the last coordinate in a site (i.e. end-start= 1 for a CpG). Sites on the negative strand are shifted by +1.
I tried to map the 2 coordinates per probe in the bed file to the genome and they do not seem to match CGs. If I shift all coordinates by +1, however, most of them (but not all) do match CGs. The problem is that the WGBS data that I have does not contain any information in the strand column, so I cannot shift coordinates depending on whether they are the positive or negative strand.
Has anyone faced the same problem?