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 |-> FastQC (raw reads) +-> Trim Galore -> Bowtie2 (genome) -> {sample}.sorted.bam | |-> unmapped read pairs -> Bowtie2 (spike-in) -> counts -> scale_factors.txt | | +-> filter (MAPQ 10, proper pairs) -> Picard MarkDuplicates | (removed) -> blacklist filter -> {sample}.filtered.bam | |-> fragment BED -> fragment bedGraph -> SEACR peaks | |-> MACS2 peaks (with --peak_caller macs2|both) | |-> FRiP vs every peak set -> {sample}.frip_mqc.tsv | +-> bamCoverage -> {sample}.normalized.bw <-- factor ---+ ``` ### Not run by this workflow - **Peak-level filtering**: `--blacklist` is applied to the BAM only. Peak files are never