pipeline-chipseqlisted

# ENCODE ChIP-seq Pipeline ## When to Use - User wants to run a ChIP-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ChIP-seq pipeline", "MACS2", "peak calling", "BWA alignment for ChIP", or "IDR" - User needs to process histone or TF ChIP-seq data following ENCODE standards - Example queries: "process my ChIP-seq FASTQs", "run the ENCODE ChIP-seq pipeline", "call peaks from ChIP-seq with MACS2 and IDR" Execute the ENCODE ChIP-seq processing pipeline from raw FASTQ files through peak calling, IDR analysis, and signal track generation. This skill provides a Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview The pipeline processes chromatin immunoprecipitation sequencing data through quality control, adapter trimming, alignment to a reference genome, filtering and duplicate removal, blacklist filtering, peak calling with MACS2, an IDR comparison for every pair of replicates, FRiP calculation, and signal track generation. The same workflow handles transcription factor (TF) ChIP-seq and histone modification ChIP-seq. The peak mode is chosen once per run with `--peak_type narrow|broad`; it applies to every sample in that run. To process narrow and broad targets together, run the workflow twice with different `--peak_type` and `--outdir` values. ## Key Literature | Reference | Journal | Year | DOI | Relevance | |-----------|---------|------|-----|-----------| | Landt et al. "ChIP-seq guidelines and practice