Difference between revisions of "ChIP-seq Analysis Pipeline"
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| + | <span style="color:red">Note: this document is a draft and still under revision.</span> | ||
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CoGe can analyze [https://en.wikipedia.org/wiki/ChIP-sequencing chromatin immunoprecipitation sequence (ChIP-seq)] using the software package [http://homer.salk.edu/homer/ Homer]. | CoGe can analyze [https://en.wikipedia.org/wiki/ChIP-sequencing chromatin immunoprecipitation sequence (ChIP-seq)] using the software package [http://homer.salk.edu/homer/ Homer]. | ||
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==Inputs== | ==Inputs== | ||
| − | + | Three FASTQ input files are required: | |
| + | * input | ||
| + | * two replicates | ||
| − | ==Workflow== | + | ==Workflow Summary== |
| + | |||
| + | # Trim FASTQ files (optional) | ||
| + | # Align FASTQ files to reference genome sequence using selected alignment software tool (GSNAP, Bowtie, etc) | ||
| + | ## Build index of reference sequence | ||
| + | ## Individually map FASTQ files to reference | ||
| + | # Create tag directories (Homer) | ||
| + | # Find peaks (Homer) | ||
| + | # Load results | ||
==Outputs== | ==Outputs== | ||
| + | |||
| + | 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. | ||
Latest revision as of 09:53, 4 March 2016
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).
Inputs
Three FASTQ input files are required:
- input
- two replicates
Workflow Summary
- Trim FASTQ files (optional)
- Align FASTQ files to reference genome sequence using selected alignment software tool (GSNAP, Bowtie, etc)
- Build index of reference sequence
- Individually map FASTQ files to reference
- Create tag directories (Homer)
- Find peaks (Homer)
- Load results
Outputs
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.
