I have an issue when it comes to visualising NGS data (ChIP-Seq). The image below represents what is currently known about occupancy of H3K4me3.
I've downloaded many different data of H3K4me3 ChIP-Seq from the EncodeProject and when I try to visualize H3K4me3 occupancy I get something like this:
Initially, I used the already uploaded BigWig and Bed files (both from mouse and human) to generate the plots. As this didn't give me the expected result, I downloaded the fastq files, aligned them to different tools and used different peakcallers. In the end, I was getting the same plot.
To plot occupancy I've used either ngsplot or deeptools.
Am I missing something here? I've used more than 20 datasets and I end up with the same graph
Thank you in advance