pipeline-cutandrunlisted

# ENCODE CUT&RUN Pipeline: FASTQ to Peaks and Signal Tracks ## When to Use - User wants to run a CUT&RUN or CUT&Tag processing pipeline from FASTQ to peaks - User asks about "CUT&RUN pipeline", "CUT&Tag", "SEACR", "spike-in normalization", or "targeted chromatin" - User needs to process CUT&RUN/CUT&Tag data with spike-in calibration and SEACR peak calling - Example queries: "process my CUT&RUN FASTQs", "run SEACR on CUT&Tag data", "normalize CUT&RUN with spike-in controls" Execute the CUT&RUN/CUT&Tag processing pipeline for targeted chromatin profiling, producing peak calls with SEACR and spike-in normalized signal tracks. ## Pipeline Overview ``` FASTQ -> Trim -> Bowtie2 align (genome) -> Filter/dedup -> SEACR peaks | | | Bowtie2 align (spike-in) Spike-in normalize Signal tracks | Scale factor calculation ``` ### ENCODE Repository - **GitHub**: `ENCODE-DCC/cutandrun-pipeline` - **Container**: `encodedcc/cutandrun-pipeline` - **This skill**: Nextflow DSL2 reimplementation for portability ## Core Tools and Versions | Tool | Version | Purpose | Citation | |------|---------|---------|----------| | Bowtie2 | 2.5.3 | Alignment (genome + spike-in) | Langmead & Salzberg 2012 | | SEACR | 1.3 | Peak calling (CUT&RUN-specific) | Meers et al. 2019 | | MACS2 | 2.2.9.1 | Alternative peak caller | Zhang et al. 2008 | | Picard | 3.1.1 | Duplicate marking | Broad Institute