I am trying to perform hierarchical clustering on RRBS data. I have selected a subset of differentially methylated CpG sites based on results of RnBeads analysis. Next I tried to use the coordinates for these sites to extract raw methylation values from .cov files (generated by bismark_methylation_extractor (https://github.com/FelixKrueger/Bismark/blob/master/bismark_methylation_extractor
) ). Sadly, these two sets of coordinates (Bismark .cov vs RnBeads sites differential methylation) dont seem to match - they seem to be shifted by 1. RnBeads data was generated based on the same .cov files.
As far as I know both RnBeads and Bismark use 1-based coordinate system, but I am likely missing something...
I will appreciate help...