CHIP-seq Pipeline Specification

Pipeline Details

• Name: CHIP-seq Pipeline
• Pipeline UUID: 16915266cd614e24a3ca183d6d86ab63
• Version: 2.0.0
• View Pipeline:
  • AWS
  • GCP

Overview

CHIP-seq Pipeline is designed for analyzing chromatin immunoprecipitation sequencing (ChIP-seq) data. It automates the complete workflow from raw reads to peak calling and quantification, providing comprehensive quality control and analysis capabilities for histone modification and transcription factor binding studies.

Key Use cases:

• Histone Modification Analysis: Mapping and quantifying histone marks across the genome to understand chromatin states and gene regulation.
• Transcription Factor Binding Site Discovery: Identifying and characterizing protein-DNA interactions through peak calling and motif analysis.
• Comparative ChIP-seq Studies: Processing multiple samples for differential binding analysis and consensus peak identification.

Features

• Comprehensive Quality Control Pipeline: Implements FastQC, adapter removal, quality filtering, and trimming with multiple tool options including Trimmomatic and Fastx toolkit.
• Flexible Read Mapping: Supports Bowtie2 alignment with sequential mapping capabilities for filtering common sequences (ERCC, RepeatMasker).
• Advanced Peak Calling: Utilizes MACS3 v3.0.1 for sensitive and specific ChIP peak detection with support for input controls.
• Duplicate Removal Options: Provides both Picard and Samtools-based duplicate removal strategies.
• Consensus Peak Analysis: Merges peaks across multiple samples using Bedtools for robust peak identification and quantification.
• UMI Support: Includes UMI extraction and deduplication capabilities for enhanced data quality.
• Comprehensive Reporting: Generates detailed QC metrics, alignment statistics, and visualization-ready files (TDF, BigWig).
• Scalable Architecture: Processes multiple samples in parallel with modular design for customization.

Input/Output Specification

Inputs

Required

Reads

• Description: Raw sequencing reads in FASTQ format from ChIP-seq experiments
• Format: .fastq.gz
• Example File Path: /path/to/input/sample_R1.fastq.gz

ChIP-prep Section

• Description: Sample definitions for peak calling with MACS3
• Required Fields: Output-Prefix, Sample-Prefix, Input-Prefix (optional)
• Format: Tab-separated configuration
• Example: | Output-Prefix | Sample-Prefix | Input-Prefix | |---------------|---------------|--------------| | exper-rep1 | exper-rep1 | | | control-rep1 | control-rep1 | |

Outputs

Reported Outputs

• Peak Count Matrix:
• Description: Quantified read counts for each peak region across all samples
• Format: .tsv
• Example File Path: /output/results/peak_counts_matrix.tsv
• Visualization App: DEBrowser

• Location: Results folder

• Individual Peak Files:

• Description: MACS3 peak calls for each sample
• Format: .narrowPeak, .xls
• Example File Path: /output/peaks/sample_peaks.narrowPeak
• Visualization App: IGV, UCSC Genome Browser
• Location: Peaks folder

Supporting Outputs

• Alignment Files:
• Description: Deduplicated BAM files with alignment indices
• Format: .bam, .bai

• Example File Path: /output/alignments/sample_dedup.bam

• Quality Control Reports:

• Description: FastQC reports, alignment statistics, and Picard metrics
• Format: .html, .pdf, .tsv

• Example File Path: /output/qc/sample_fastqc.html

• Genome Browser Files:

• Description: Signal tracks for visualization
• Format: .tdf, .bigwig
• Example File Path: /output/tracks/sample_signal.tdf
• Visualization App: IGV, UCSC Genome Browser

Associated Processes

• Add custom seq to genome gtf
• Adapter Removal
• Adapter Removal Summary
• ATAC CHIP summary
• bed merge
• bedtools coverage
• Bowtie Summary
• Check BED12
• Check Build Bowtie2 Index
• check Bowtie2 files
• check files
• Check Genome GTF
• Check chrom sizes and index
• Check Sequential Mapping Indexes
• ChIP ATAC seq Reporting
• ChIP MACS
• ChIP Prep
• convert gtf attributes
• Deduplication Summary
• deepTools CreateMatrix
• deepTools PlotHeatmap
• Download build sequential mapping indexes
• FastQC
• FastQC after Adapter Removal
• HOMER Annotate Peaks
• HOMER Motif Finder
• IGV BAM2TDF converter
• Map Bowtie2
• Merge Bam
• Merge TSV Files
• MultiQC
• Overall Summary
• Picard
• Picard MarkDuplicates
• Picard Summary
• Quality Filtering
• Quality Filtering Summary
• Remove Multimappers with Samtools
• RSeQC
• Sequential Mapping
• Sequential Mapping Bam count
• Sequential Mapping Summary
• Trimmer
• Trimmer Summary
• UCSC BAM2BigWig converter
• UMIextract
• Umitools Summary

References & Additional Documentation

• Related Papers:
• Yukselen, O., Turkyilmaz, O., Ozturk, A.R. et al. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x
• DOI: 10.1186/s12864-020-6714-x
• Program Versions: MACS3 v3.0.1, Bowtie2 v2.3.5, FastQC v0.11.8, Picard v2.18.27, Samtools v1.3, MultiQC v1.7, Trimmomatic v0.39, Bedtools v2.29.2