Software for motif discovery and ChIP-Seq analysis

This is the old version of the documentation: New Version

ChIP-Seq Analysis

ChIP-Seq is the best thing that happened to ChIP since the antibody.  It is 100x better than ChIP-Chip since it escapes most of the problems of microarray probe hybridization.  Plus it is cheaper, and genome wide.  Chuck would be pleased if he came up with the idea.

HOMER offers solid tools and methods for interpreting ChIP-Seq experiments.  In addition to UCSC visualization support and peak finding [and motif finding of course], HOMER can help assemble data across multiple experiments and look at positional specific relationships between sequencing tags, motifs, and other features.  You do not need to use the peak finding methods in this package to use motif finding. (Use the bed2pos.pl program to create peak files from BED files).

NOTE:  The current implementation is geared for single tag sequencing.


Standard ChIP-Seq analysis with HOMER:

  1. Creating a "Tag Directory" from aligned sequences
  2. Basic quality control (sequence bias, fragment length estimation)
  3. Creating files to view your data in the UCSC Genome Browser
  4. Finding Peaks (ChIP-enriched regions) in the genome
  5. Finding enriched motifs in ChIP-Seq peaks
  6. Annotating Peaks (and cross referencing other experiments and motifs)
Automating standard ChIP-Seq analysis with analyzeChIP-Seq.pl

Advanced ChIP-Seq Analysis with HOMER:

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