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chip-seq-pipeline's Introduction

CCBR ChIP-Seq Pipeline

Installation

  1. install nextflow

    curl -fsSL get.nextflow.io | bash

    For details, visit https://www.nextflow.io/

  2. clone this git repository

    #for latest experimental features
    git clone https://github.com/CCBR/ChIP-Seq-Pipeline.git

    For the stable version of the pipeline, download from the following link https://github.com/CCBR/ChIP-Seq-Pipeline/releases/latest

How to run the pipeline

./nextflow run main.nf \
	-config config \
	--macsconfig='example/macs.config' \
	--reads='example/*.fastq' \
	--genome='hg19'
  • Note that the reads names are supposed to end with ".fastq" or ".fastq.gz". If you experience an error message related to missing file(s), this might be the reason.

  • Config file is designed to work at our NIH biowulf2 HPC. If you plan to use on helix, add -profile 'local' option at the end of command line arguments. If you plan to use outside NIH, you need to edit the "genome" section according to your paths information.

  • macs.config is a config file for MACS2 to find peaks. ChIP sample and control (input or IgG) with their label concatenated by comma form a line, e.g. chip_sample_id,control_id,sample_name. chip_sample_id or control_id are the basename of the FASTQ files wihtout the trailing ".fastq" or ".fastq.gz".

  • Currently, the pipeline fully supports hg19, mm10 and partially supports GRCh38 and GRCm38. Contact us for other genomes.

Additional options:

  • -resume --> to resume the previous failed run
  • -profile 'local' --> for running tools "locally" not thourgh high performance computer queueing mechanisms.
  • -with-timeline 'timeline.html' --> record the run time of each process.
  • -with-dag 'flowchart.png' --> draw the flowchart
  • --outdir 'ChIP-Seq-Pipeline-Output' --> specify the directory to save directory from the default output

We implemented the pipeline using Nextflow.

Implemented tools

Thanks to the authors of the tools!

  1. Trimgalor
  2. BWA mem
  3. Picard (MarkDuplicate)
  4. FASTQC
  5. DeepTools
  6. Macs2
  7. Sicer
  8. MEME-ChIP
  9. PhantomPeakqualTool
  10. CEAS

Todo list

  1. ChipSeeker
  2. Homer
  3. PeakDiff
  4. ngsplot

Thanks

I got many nice implementation ideas from Nextflow examples, especially from NGI-ChIP-seq pipeline. Many thanks to the NGI pipeline developers and Alexei, Ashley, George, Parthav and other CCBR team mebers.

Questions or Suggestions

Email to Bong-Hyun.Kim at NIH dot GOV.

chip-seq-pipeline's People

Contributors

joshuabhk avatar

Watchers

James Cloos avatar Wei Tang avatar

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