I have some peaks in my ChIP data where the height is eg. 100, and the input at the same site is also around 90-100. These sites tend to be at regions with low mapability and/or repeat sequences, as shown with the mapability and repeat masker tracks in the UCSC browser. I assume these peaks are background and don't consider them real.
I have other sites which will also have a height of 100 and the input will have what looks like a small peak, maybe 10-15, while the input for the rest of the region is <5. Sometimes the IP peak is really big, like 200-300 and the input is maybe 20. These sites are generally in regions with no problems such as repetitive sequences.
Can I consider this second group of peaks, the ones that have a small input peak, as real? Maybe they're real but just not quite as high as they appear in the IP sample, ie. some of the enrichment in the region is background but most is real?
I have other sites which will also have a height of 100 and the input will have what looks like a small peak, maybe 10-15, while the input for the rest of the region is <5. Sometimes the IP peak is really big, like 200-300 and the input is maybe 20. These sites are generally in regions with no problems such as repetitive sequences.
Can I consider this second group of peaks, the ones that have a small input peak, as real? Maybe they're real but just not quite as high as they appear in the IP sample, ie. some of the enrichment in the region is background but most is real?
Comment