ChIP-seq Analysis Pipeline

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).

Inputs

Three FASTQ input files are required:

• input
• two replicates

Workflow

1. Trim FASTQ files (optional)
2. Align FASTQ files to reference genome sequence -- these steps depend on which alignment software tool is selected (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