I'm not a bionformatician but I follow Biostar closely in my quest to learn some meaningful basics of NGS analyses. I performed a chip-seq experiment lately looking at histone markers H3K27ac and H3K4me1 on very small amount of chromatin originating from minute tissue samples. I used HOMER for the analyses and it reported 'low enrichment with high background' for both samples. This is reflected on the profiles when viewed on the UCSC browser. My colleague who is a trained bioinformatician used MACS and reported the same. We did however obtained number of called peaks (or significant peaks vs. input) similar to those reported in the literature and I'm currently investigating these.
Does anyone know of any methods that can be used or applied to my case to enrich for 'true' peaks vs background? And, to be able to view these peaks clearly and distinctively from 'background' on the UCSC browser?
Appreciate any help or advice given.