Hi,
I used CCAT to call peaks for the H3k4me3 mark in my samples and the average peak width I noticed is ~3kb
I wanted to get a sense check on these nos. ? Usually in cancer samples, is that the sort of profile that is seen for H3k4me3. I tried looking this up in literature but I dint get enough data pts and the few that I did showed an average profile of 1.5kb.
Does anybody have any references on this ?
Thanks !
Hi Sukhdeep.. Thanks for this.. This gives me some consolation. The peaks im looking at are infact active promoter regions and some of my peaks even go up to 5kb or 8kb. Makes me wonder if taking a union of overlapping peaks is a good idea ? Are promoter regions really that long or Im lumping them all and missing out on information..
There might be different cases why the peak looks broad
Cheers
Do you know why H3K3me3 shows a small peak before the TSS and a more sharper peak after TSS?