Hi! I am counting ChIP-seq files and comparing the whole-genome binding peaks of two proteins. I see a low over-lap on heat maps (less than 10% and strong peaks of 1 protein overlap with not strongest or weak peaks of 2nd protein), but when I use "bedtools Intersect intervals" tool it gives me a peaks that I don't see in IGV after making bigwig files. How can I set up the threshold to remove such false peaks from counting. I tried to set Mapq 40 instead of 5 while filtering Bam files, but nothing actually changed. Also I tried different ways to count bigwigs, but the peaks present in bed files are not visible in bigwigs.
I suggest that the peaks that overlap are not important, but want to find a way to remove them from the count list. Would be great if you could help me. Thank you in advance, Sincerely, Mary