Time: 1.5 hours

This is a demonstration of ATAC-Seq data analysis starting with the import of raw sequencing .fastq files, followed by alignment to the reference genome, peak detection, and annotation. Comparing peaks between different groups with multiple replicates is introduced. Motif detection is performed on significant regions and interpretation of the biology by conducting KEGG pathway enrichment analysis on genes overlap regions.

• Import fastq files
• Attribute management
• QA/QC
• Alignment
• Detect enriched regions with MACS2
• Annotate regions
• Compare regions among different groups
• Search for motifs on significant regions
• KEGG enrichment analysis

Visualization: scatterplot, TSS plot, volcano plot, heatmap etc.