ChIP-seq Analysis Pipeline: Difference between revisions
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## Build index of reference sequence | ## Build index of reference sequence | ||
## Individually map FASTQ files to reference | ## Individually map FASTQ files to reference | ||
# Create tag directories (Homer) | |||
# Find peaks (Homer) | |||
# Load results | |||
==Outputs== | ==Outputs== | ||
Revision as of 21:46, 3 March 2016
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
- Trim FASTQ files (optional)
- Align FASTQ files to reference genome sequence -- these steps depend on which alignment software tool is selected (GSNAP, Bowtie, etc)
- Build index of reference sequence
- Individually map FASTQ files to reference
- Create tag directories (Homer)
- Find peaks (Homer)
- Load results