![[Pasted image 20250221012848.png|300]] # ATAC Sequencing ## Peak Calling The peak calling process Certain regions of genomes have been shown to be problematic when included during the peak calling step. It may be useful to *blacklist* these regions, or create a *subset* with only the regions under investigation. Once identified, peaks have a signal level associated with them which describes the magnitude of the read counts associated with the peak. ### Peak Centered Heatmaps ![[Pasted image 20250307061005.png|450]] The heatmap and composite profiles summarize your data around transcription start sites (TSSs) and annotated genes. This allows you to visually asses the overall quality of your ChIP-Seq data, including enrichment of your target over background and its binding pattern relative to genes.