I've been looking all over the internet and haven't found an answer to this question yet so hopefully someone can help me out. I used the DiffBind package in R to identify regions that have different histone markings from some ChIP-seq data between two experimental conditions. Everything worked great, but for publication purposes I would love to show some browser shots of candidate genes. I can load the raw reads into a browser, but I would prefer to have them scaled to the normalization factors that DiffBind used at each locus to better show difference in binding profiles. Even better would be to convert the normalized counts and plot the fold changes from one condition to the next at some regular interval. Any idea how to do this? Particularly how to get the locus specific normalization factors?
PS - I am a novice on R and if it wasn't for their well-written vignette, I would not have gotten this far, so please explain any answers to me in simple terms - Thanks!