ChIP-seq Analysis Pipeline

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Note: this document is a draft and still under revision.

CoGe can analyze chromatin immunoprecipitation sequence (ChIP-seq) using the software package Homer.

See the LoadExperiment tool to use the new pipeline.

This analysis pipeline was developed by Xiang Ju (in the lab of Brian Gregory at UPenn).


Three FASTQ input files are required:

  • input
  • two replicates

Workflow Summary

  1. Trim FASTQ files (optional)
  2. Align FASTQ files to reference genome sequence using selected alignment software tool (GSNAP, Bowtie, etc)
    1. Build index of reference sequence
    2. Individually map FASTQ files to reference
  3. Create tag directories (Homer)
  4. Find peaks (Homer)
  5. Load results


The pipeline produces 5 outputs (represented as "Experiments" in CoGe):

  • Three BAM files corresponding to each FASTQ input mapped to the reference genome sequence
  • Two peaks tracks corresponding to the input analyzed with respect to each replicate.