I am trying to find the consensus peaks of a 8 samples of chip-sea peaks data. The format is Bed.I am not having any problems with finding the overlapping peak coordinates with thankfully bedtools multiinter function. However, when the functions find the overlaps across 8 samples, the peak values are excluded. I just want to do a normalisation or an averaging for a specific overllaped peak value across the samples.
I am looking for the effect of the transcriptional factors on a chromosomal rearragements thats why I need those TF binding coordinates.
PS: I have used other overlapping programs such as Homer an bedops. None of them has that value normalisation feature. This cannot be a coincidence ?
thank you very much for your help.