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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
Use with AI
Install the MCP server or CLI to instantly fetch ENCODE Pipeline ATAC-seq documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/encode-pipeline-atac-seq
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
1 shared topic • 3 shared operations
bamutil — C++ toolkit for reading, writing, and manipulating BAM alignment files. Provides duplicate marking (dedup), base quality score recalibration (recab), overlapping read clipping (clipOverlap),
1 shared topic • 2 shared operations
methylpy — Python pipeline for whole-genome bisulfite sequencing (WGBS) methylation analysis. Trims adapters, aligns with Bowtie2, marks duplicates, and calls cytosine methylation in CpG, CHG, and CHH
1 shared topic • 2 shared operations
nf-core/atacseq — Nextflow pipeline for ATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) data analysis. Handles paired- or single-end reads through adapter trimming (Trim Galore),
1 shared topic • 2 shared operations
PinAPL-Py (Pooled In/out Screen Analysis Pipeline for Python) is a complete analysis pipeline for pooled CRISPR sgRNA screens. Handles raw FASTQ alignment to sgRNA libraries, read counting, normalizat
1 shared topic • 2 shared operations