How to calculate correlation coefficient for chipseq?

Question

[Emily]

If I want to see if my transcription factor chipseq correlate with a histone mark chipseq, is this a common practise: bamcompare to get the bigwig file with fold enrichment and then use bigwigsummary and plotcorrelation?

But this method gave me very low correlation coefficient, even the histone mark showed more than 40% of overlapping peaks with my called peaks and showed similar pattern in IGV with my chipseq data.

Are there other methods? As I saw most study calculating coefficient using called peaks but not sure how to do that.