I apologies for posting yet another beginners question about ChIP-seq. I don't have a bioinformatician to hand to help me so I really rely on you guys and this site to teach me how to analyse my data. Thank you in advance!
I have some ChIP-seq data (input control and IP sample) that I'm running with MACS2 (version 2.1.0) in Galaxy. I've managed to generate peaks and all the usual output files (peak.xls, peak.bed, treatment.bedgraph, control.bedgraph, narrow peaks.tab, summits.bed etc etc). From reading around here, it seems a good thing to do next is to take a look at my peaks in a genome browser. When I look at my two bedgraph files in IGB, I see peaks in my IP which is fine. However, if I then look at the peaks.xls file of my called peaks, they don't seem to reflect what I'm seeing in the IGB browser at all. For example, if I zoom into a co-ordinate that's in my peak.xls file in my bedgraph files on IGB I don't see a peak and vice versa, when I see what looks like a valid peak in IGB, it isn't called in my peak.xls file.
Can someone please point out to me what I'm misunderstanding here? I understand that sometimes called peaks aren't obvious to the eye as there are various normalizations to background and statistical modelling going on behind the scenes to call them, but still, mine aren't convincing me at all.
Have I missed a step, am I looking at the wrong files, or completely misinterpreting something (or all 3)?