Through a collaborator I have received bw files from bisulphite sequencing which give me information regarding methylation percentages for cytosine residues. I need to correlate them with chipseq data for a transcription factor. I haven't worked with methylation data before and thus I am unable to understand how can I get it in a form amenable to correlation analysis.
I think I cannot just do a correlation using deeptools computeMatrix as it will do an average over the window for methylation bw and that is not what is needed here. The other options of median, min, max, std, sum also dont make much sense. Is there a tool that will into account possible sites that could be potentilly methylated in a window and then gives me a value to be used for correlation.
Any general pointers towards doing methylation and chip-seq correlation may be useful too.
