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. To facilitate the analysis, it is useful to transform the sequence alignment into platform independent data structure. HOMER does this by creating a "Tag Directory" with makeTagDirectory to place all relevant information into a "Tag Directory". It takes alignments files as input in the following formats, BED, SAM, BAM, default bowtie output, and TXT froth Illumina pipeline (this AGAVE app only wraps the first three formats). HOMER will use "samtools view file.BAM > file.SAM" to covert to a SAM file, so "samtools" must be available. If the alignment is in a different format, it is recommended to convert it into BED format.




  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Input alignment folder
    2. Output folder
  3. Optional arguments:
    1. -tbp: maxium tags per bp
    2. -format: format of the alignment files
    3. -single: setting this option will place all reads into a single tag file instead of separate tag files for each chromosome

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. Inputs:
    1. G3_P_H3_rep1_chr8_rmDup.sorted.bam
    2. G3_P_H3_rep2_chr8_rmDup.sorted.bam
    3. G3_P_K4me3_rep1_chr8_rmDup.sorted.bam
    4. G3_P_K4me3_rep2_chr8_rmDup.sorted.bam
    Note: These are outputs of Picard_MarkDup-2.7.0.
  2. -tbp: 1
  3. -format: BAM
  4. -single: TRUE



Successful execution of the "makeTagDirectory" will create a directory named "homerTagDir" by default including the tag directory for each alignment input. 


  1. homerTagDir (test data outputs)
    1. G3_P_H3_rep1_chr8_R_rmDup_tagDir
    2. G3_P_H3_rep1_chr8_R_rmDup_tagDir
    3. G3_P_K4me3_rep1_chr8_R_rmDup_tagDir
    4. G3_P_K4me3_rep2_chr8_R_rmDup_tagDir




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