Using ATAC-Seq to identify open chromatin

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a method to identify regions of accessible ("open") chromatin that are presumed to be available for binding by transcription factors and other DNA-binding proteins, which in turn can regulate genome function. It can help answer experimental questions previously addressed by techniques like MNase-seq, DNase-Seq, and FAIRE-Seq.

Basic Approach

• Pre-process reads (remove adapters and other "contamination")
• Map reads to the genome (with an unspliced mapping tool)
• Run quality control and calculate QC metrics
• Identify ATAC-seq "peaks" with a high coverage of mapped reads
• Analyze peak regions for binding motifs
• [For multiple-sample experiments] Identify differentially accessible regions
• Identify potential targets of peak regions and/or differentially accessible regions