Peak Calling Analysis

Package Overview

Goal

Identification of peaks for bulk ATAC-seq, ChIP-seq, CUT&RUN and CUT&Tag data

Requirements

• none

Analysis

• Running the nfcore pipelines (look for “Pipeline Summary”)
  • nfcore/atacsseq for ATAC-seq data (fork of the original pipeline with a local fix)
  • nfcore/chipseq for ChIP-seq data
  • nfcore/cutandrun for CUT&RUN and CUT&Tag data
• In brief, the pipelines include (but are not limited to):
  • Adapter trimming
  • Mapping to reference genome(s)
  • Creating bigWig coverage files
  • Peak calling
  • Creating IGV Genome Browser session

Output

• The nfcore pipelines produce the most important output files (look for “output” documentation in the above links):
  • BAM and bigWig files
  • Peak bed files
  • IGV session file
  • MultiQC HTML report

Advanced Analysis

• Transcription factor binding sites (Homer)
  • Find enriched TFBSs in peaks
  • For TFBSs of interest, find specific instances of binding in peaks
• Differential analysis (at least 3 replicates required)