pipeline-dnaseseqlisted

# ENCODE DNase-seq Pipeline: FASTQ to Hotspots and Footprints ## When to Use - User wants to run a DNase-seq processing pipeline from FASTQ to hotspots and footprints - User asks about "DNase-seq pipeline", "DNase hypersensitive sites", "Hotspot2", "footprinting", or "DHS" - User needs to process DNase-seq data for chromatin accessibility and TF footprint analysis - Example queries: "process my DNase-seq FASTQs", "call DNase hypersensitive sites", "run footprinting analysis on DNase-seq" Execute the ENCODE DNase-seq pipeline for chromatin accessibility profiling, producing DNase hypersensitive sites (DHSs) via Hotspot2 and transcription factor footprints. ## Pipeline Overview ``` FASTQ -> Trim -> BWA-MEM align -> Filter/dedup -> Hotspot2 -> DHS peaks | | Signal track Footprinting (HINT) ``` ### ENCODE Repository - **GitHub**: `ENCODE-DCC/dnase-seq-pipeline` - **Container**: `encodedcc/dnase-seq-pipeline` - **WDL**: Available for Cromwell execution - **This skill**: Nextflow DSL2 reimplementation for portability ## Core Tools and Versions | Tool | Version | Purpose | Citation | |------|---------|---------|----------| | BWA-MEM | 0.7.17 | Alignment | Li & Durbin 2009 | | samtools | 1.19 | BAM operations | Li et al. 2009 | | Picard | 3.1.1 | Duplicate marking | Broad Institute | | Hotspot2 | 2.3.1 | DHS calling (ENCODE standard) | John et al. 2011 | | bedtools | 2.3