Introduction

nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) and assay for transposase accessible chromatin (ATAC-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)
• Build BED reference based on GTF (optional)
• Build genome size table for bedToBam conversion (optional)
• FastQC for initial quality control of sequence reads
• TrimGalore! for adapter trimming
• BWA for alignment
• Samtools for post-alignment processing with and alignment statistics
• Picard MarkDuplicates for duplicate removal
• Count read statistics
• Phantompeakqualtools for NSC, RSC and strand-shift cross correlation plot
• DeepTools for paired-end fragment size distribution, fingerprint, reads distribution profile, sample pair-wise correlation, and PCA plot.
• MACS2 for peak calling
• MACS2 for saturation analysis (optional)
• Bioconductor ChIPpeakAnno for 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).