The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to xwang@cshl.edu. Thank you.

Rationale and background:

HOMER: Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz S, Benner C, Spann N, Bertolino E et al.

Mol Cell 2010 May 28;38(4):576-589. [PMID: 20513432]



HOMER is a collection of tools for NGS (next-generation sequencing) data analysis. It offers tools and methods for interpreting numerous types of functional genomics sequencing data, such as ChIP-Seq, GRO-Seq, RNA-Seq, Hi-C, and ect. Annotation regions (annotatePeak.pl) in HOMER is a useful, all-in-one program to performing peak annotation in genome. In addition, annotatePeaks.pl can perform Gene Ontology Analysis, genomic feature association analysis (Genome Ontology), associate peaks with gene expression data, calculate ChIP-Seq Tag densities from different experiments, and find motif occurrences in peaks.  annotatePeaks.pl can also be used to create histograms and heatmaps.  Description of the annotation functions are covered here, while quantification of tags, motifs, histograms, etc. are referred here.




  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Inputs: Peak files to be annotated, annotatePeaks.pl accepts HOMER peak files or BED files.
  3. Optional arguments:
    1. -Reference Fasta: For organisms with relatively incomplete genomes, annotatePeaks.pl can still provide some functionality.  If the genome is not available as a pre-configured genome in HOMER, then you can supply the path to the full genome FASTA file or path to directory containing chromsome FASTA files as the 2nd argument.
    2. -Genome Anno File (using custom annotations): 
      HOMER can process GTF (Gene Transfer Format) files and use them for annotation purposes ("-gtf <gtf filename>"). 
      You may also find a custom annotation file for the organism, such as banana_slug_genes.gtf, or banana_slug_genes.gff from the community website. 
    3. -Gene Expression Data: annotatePeaks.pl can add gene-specific information to peaks based on each peak's nearest annotated TSS.  To add gene expression or other data types, first create a gene data file (tab delimited text file) where the first column contains gene identifiers, and the first row is a header describing the contents of each column.  In principle, the contents of these columns doesn't mater. 
    4. -GENOME: Pre-configured genome in HOMER, e.g. hg18.

Test with sample data

The following test data are provided for testing HOMER_annoPeaks-4.8.3 here /iplant/home/xiaofei_iplant/Sorghum_chr8/chr8_test:

  1.  G1_P_K4me3_interSect.bed

Note: This could be the output of  intersectBed-2.26.0 or HOMER_findPeaks_4.8.3.


Successful execution of the "annoPeaks" will create a file for annotating peaks.


  1. Peak annotation file:
    e.g., homerPeakAnno/G3_P_K4me3_interSect_PeakAnno.txt


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