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| | 2 | == Using ATAC-Seq to identify open chromatin == |
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| | 5 | 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. |
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| | 7 | Basic Approach |
| | 8 | * Pre-process reads (remove adapters and other "contamination") |
| | 9 | * Map reads to the genome (with an unspliced mapping tool) |
| | 10 | * Run quality control and calculate QC metrics |
| | 11 | * Identify ATAC-seq "peaks" with a high coverage of mapped reads |
| | 12 | * Analyze peak regions for binding motifs |
| | 13 | * [For multiple-sample experiments] Identify differentially accessible regions |
| | 14 | * Identify potential targets of peak regions and/or differentially accessible regions |
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