Methylation level assessment in published Bi-Seq data

Question

[JulianC]

Hi!

I am working on published Bi-Seq data, that are presented in the following way:

Chr    Start   End   Total   5meCpG
chr1   31567   31569   41    20
chr1   31582   31584   91    89
chr1   31603   31605   26    25

My goal is to assess the methylation level within the promoter of some genes of interest. Since it is not reported the annotation for these coordinates, I am using Homer annotatePeaks.pl to do it. Homer forced me to indicate the strand (+ or -), and from the description I found in NCBI GEO page relative to the paper I am dealing with, they state that CpG positions and total coverage and methylated coverage are obtained by combining both strands. I used Homer twice, first with all + and then with all -. Then I simply divided the 5meCpG values to the Total in order to obtain the methylation level. I realized that, at least for promoter regions, I got the same annotation for both runs ( all + and all -). Is this procedure correct? Should I operate in a different way? Thank you in advance!

[Devon Ryan]

I'd be surprised if you got any notable difference there. Personally I would have just used bedtools nearest.