empty peaks count, ChIP-seq, filter Bam, bed, bigwig, threshold, false peaks

Question

[maverenia]

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

Answer 1

[maverenia]

For the MACS2 callpeak I use the following conditions: Set lower mfold bound - 5 Set upper mfold bound - 50 Band width for picking regions to compute fragment size - 350 Peak detection based on q-value Minimum FDR (q-value) cutoff for peak detection - 0,01

Thanks in advance!

Answer 2

[maverenia]

I quess the problem is that I don't see the weak peaks in bigwigs, but they are counted in bed files. I there some approach to get bigwigs to be exactly comparable with beds? Thanks!