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 complete Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview The ENCODE ChIP-seq pipeline processes chromatin immunoprecipitation sequencing data through a series of well-defined stages: quality control, adapter trimming, alignment to a reference genome, filtering and deduplication, peak calling with MACS2, replicate consistency analysis via IDR, and signal track generation. Each stage is parameterized according to ENCODE standards and produces QC metrics for comprehensive quality assessment. This pipeline handles both transcription factor (TF) ChIP-seq and histone modification ChIP-seq, automatically selecting narrow or broad peak calling modes as appropriate. ## Key Literature | Reference | Journal | Year | DOI | Relevance | |-----------|---------|------|-----|-----------| | Landt et al. "ChIP-seq guidelines and practices" | Genome Research | 2012