Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding. Here we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from “gold standard” CUT&RUN…

• HH
  Howard Hughes Medical Institute

  Award: TCPA A093
• NI
  National Institutes of Health

  Award: 4DN TCPA A093
• NH
  National Human Genome Research Institute

  Award: 1R01HG010492