I am new to this and have used MACS for peak calling and I now want to annotate the peaks. I am not sure which tool I should be using for this. I performed ChIP to investigate histone modifications looking at HDAC1 and 2. In theory I think I should be finding peaks (or lack of peaks) at the promoter regions of genes. I have used rat tissue. I have downloaded the rat UCSC file but I am not sure what to do next?
The second part of my question is that I want to compare regulated regions between samples, I have 2 treatments and a control sample and want to see which genes are more or less regulated by HDAC1 and 2 in these samples. What tool should I be using to compare between them all?
Thanks for your help,