Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
Switch branches/tags
Nothing to show
Clone or download
#55 Compare This branch is 107 commits ahead, 3 commits behind SciLifeLab:master.
ewels Merge pull request #42 from Rotholandus/master
Missing likns fixed in usage.md
Latest commit 5f67d82 Aug 10, 2018

README.md

nf-core/chipseq

Build Status Nextflow Gitter

install with bioconda Docker Container available https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg

Introduction

nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

Pipeline Steps

  • Make BWA reference genome index (optional)
  • FastQC
  • TrimGalore!
  • Align with BWA
  • Samtools sort, index, stats & convert to BED
  • Samtools idxstats
  • Picard MarkDuplicates
  • Count read statistics
  • PhantomPeakQualTools
  • SPP: Calculate NSCRSC and cross correlation
  • DeepTools bamPEFragmentSize, plotFingerprint, bamCoverage, multiBamSummary, plotCorrelation, plotPCA
  • NGSplot
  • MACS2 peak calling
  • Saturation analysis
  • ChIP peak annotation
  • MultiQC

Documentation

The nf-core/chipseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation and configuration
  2. Running the pipeline
  3. Output and how to interpret the results

Credits

These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. Written by Chuan Wang (@chuan-wang) and Phil Ewels (@ewels).