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ENCODE ChIP-seq pipeline — official ENCODE DCC WDL/Cromwell pipeline for transcription factor (TF) and histone mark ChIP-seq analysis. Handles adapter trimming (Trimmomatic), alignment (Bowtie2/BWA),
Use with AI
Install the MCP server or CLI to instantly fetch ENCODE Pipeline documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/encode-pipeline-chip-seq
Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short
1 shared topic • 2 shared operations
nf-core/chipseq — Nextflow pipeline for comprehensive ChIP-seq analysis from raw reads through peak calling and differential analysis. Automates adapter trimming, multi-aligner support (BWA, Bowtie2,
1 shared topic • 2 shared operations
Cell Ranger ATAC — 10x Genomics official pipeline for processing single-cell ATAC-seq (scATAC-seq) data from raw FASTQ files to peak-barcode matrices and fragment files. Performs barcode demultiplexin
3 shared operations
CUT&RUNTools 2.0 — end-to-end analysis pipeline for CUT&RUN and CUT&TAG chromatin profiling experiments. Handles adapter trimming (Trimmomatic), spike-in normalization, Bowtie2 alignment with size-sel
3 shared operations
ENCODE DCC ATAC-seq pipeline — ENCODE consortium-standard WDL/Cromwell pipeline (run via Caper) for processing bulk ATAC-seq data from FASTQ through alignment, deduplication, peak calling (MACS2), IDR
3 shared operations