Fig. 2
From: From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Roadmap of a typical ATAC-seq analysis. Four major steps are listed, including pre-analysis, core analysis, advanced analysis, and integration with multiomics data. Pre-analyses include pre-alignment QC, alignment and post-alignment processing, and QC. Core analysis includes peak calling. Advanced analyses include peak, motif, footprint, and nucleosome analysis. Multiomics data integration includes integration with ChIP-seq and RNA-seq data and regulatory network reconstruction. Text in each box emphasizes the important considerations in each analysis step. We suggest researchers start with FastQC, trimmomatic, and BWA-MEM for pre-analysis, MACS2 for peak calling, csaw for peak differential analysis, ChIPseeker for annotation and visualization, MEME suite for motif detection and enrichment, HMMRATAC for nucleosome detection, HINT-ATAC for footprint analysis, and PCEA for regulatory network reconstruction with RNA-seq. QC: quality check; TSS: transcription start site; TF: transcription factor; DEG: differentially expressed gene