Maybe this is a silly question. I have several peaks called with macss (n = 12808) and I want to create two groups based peaks at transcribed genes and peaks at not transcribed genes. My first approach is to annotate peaks with Chipseeker , which gaves me a total of n = 12576 peaks, so I can consider those peaks at transcribed genes. In order to identify the peaks at not trasncribed genes, my idea is use
bedtools intersect -v and the remaining 232 peaks would be consider as not trasncribed. Is this a good approach? or do you guys have any better idea?