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HOMER Annotate Peaks Specifications

Process Details

  • Name: HOMER Annotate Peaks
  • Process UUID: ccf64bf681f04f0bbd6c19572a558bd2
  • Process Group: Misc.

Overview

HOMER Annotate Peaks is a genomic annotation process that assigns biological context to peak coordinates from ChIP-seq, ATAC-seq, or other peak-calling experiments. Using the HOMER 5.1 toolset's annotatePeaks.pl tool, this process takes peak coordinates and annotates each peak with comprehensive genomic information including nearby genes, distance to transcription start sites (TSS), genomic features (promoter, exon, intron, intergenic regions), and detailed transcript annotations. This annotation provides critical context for interpreting the potential regulatory roles of peaks and serves as a foundation for downstream analyses such as motif discovery and functional enrichment studies.

This process is implemented in Bash, which invokes the HOMER annotatePeaks.pl Perl script for genomic annotation.

Key Functionality

  • Genomic Context Assignment: Annotates peaks with their genomic locations relative to genes, promoters, exons, introns, and intergenic regions
  • Gene Association: Links each peak to nearby genes and calculates distances to transcription start sites (TSS)
  • Comprehensive Annotation: Provides detailed genomic feature information including transcript IDs and regulatory element classifications
  • Quality Reporting: Reports peaks that cannot be associated with known genomic features with appropriate NA values

Input/Output Specification

Inputs

Required Inputs

  • Peak Coordinates

    • Description: Peak coordinates from ChIP-seq, ATAC-seq, or similar experiments
    • Format: BED format

  • Reference Database Directory

    • Description: Directory containing HOMER genome database files and configuration
    • Format: Directory containing genome annotation files

Outputs

  • Annotated Peaks
    • Description: Comprehensive annotation file containing peak coordinates with associated genomic context, gene information, distances to TSS, and genomic feature classifications
    • Format: TXT (tab-delimited)

References & Resources

  • Tool Documentation: Contact the team for details on annotatePeaks.pl
  • Related Papers: Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38, 576-589 (2010). DOI: 10.1016/j.molcel.2010.05.004