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. Among of a suit of tools, finding peaks is one of the central goals for ChIP-Seq or DNase-Seq. The basic idea is to identify the genome regions with enrichment where more sequencing reads are expected to see by chance. HOMER can handle different types of genomics sequencing data by specializing specific analysis strategies, such as transcription factor, histone modification, de novo transcript identification from GroSeq, TSS identification from 5' RNA-Seq, and ect.




  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Tag directory for mark of interest 
    2. Tag directory for input background (use an input or IgG as a control is highly recommended)
  3. Optional arguments:
    1. -STYLE: specify an analysis strategy
      1. factor
      2. histone
      3. groseq
      4. gss
      5. dans
      6. super
      7. mC
    2. -Peak Size: peak size
    3. -minDist: maximum distance used to stitch peaks together
    4. -gsize: effective mappable genome size
    5. -region: stitch adjacent enriched peaks into regions
    6. -rep: biological replicates, self-defined rather than HOMER, the name of the tag dirctory should contain "rep" followed by a number (e.g.:G3_P_H3_rep1_tagDir)

Test with sample data

The following test data are provided for testing BWA-index-mem here /iplant/home/xiaofei_iplant/Sorghum_chr8/chr8_test:

  1. Mark of interest tag directory: 
    1. G3_P_K4me3_rep1_chr8_R_rmDup_tagDir
    2. G3_P_K4me3_rep2_chr8_R_rmDup_tagDir
  2. Input control tag directory: 
    1. G3_P_H3_rep1_chr8_R_rmDup_tagDir
    2. G3_P_H3_rep2_chr8_R_rmDup_tagDir



Successful execution of the "findPeaks" will create a directory "homerPeaks" holding the HOMER peak files and a directory "homerBed" containing the peaks in BED format.


  1. homerPeaks:
    1. G3_P_K4me3_rep1_chr8_R_rmDup.txt
    2. G3_P_K4me3_rep2_chr8_R_rmDup.txt
  2. homerBed:
    1. G3_P_K4me3_rep1_chr8_R_rmDup.bed
    2. G3_P_K4me3_rep2_chr8_R_rmDup.bed



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