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Cell Ranger ATAC Pipeline Specification

Pipeline Details

  • Name: Cell Ranger ATAC Pipeline
  • Pipeline UUID: f931x0pidhba52ht192d07br3swx0w
  • Version: 1.2.1
  • View Pipeline:

Overview

Cell Ranger ATAC Pipeline is designed for processing Chromium Single Cell ATAC-seq data. It automates read alignment, barcode counting, peak detection, cell calling, and downstream analysis including clustering and differential accessibility analysis to ensure reliable and reproducible single-cell chromatin accessibility results.

Key Use cases:

  • Single-cell chromatin accessibility analysis: Process 10x Genomics Chromium Single Cell ATAC-seq data from raw FASTQ files to peak-barcode matrices.
  • Multi-library aggregation: Combine multiple Cell Ranger ATAC count outputs into a single analysis for comparative studies.
  • Quality control assessment: Generate comprehensive QC reports for ATAC-seq data quality evaluation and sample assessment.

Features

  • Support for Multiple ATAC Versions: Compatible with both ATACv1 and ATACv2 chemistry formats from 10x Genomics.
  • Comprehensive ATAC Analysis: Includes read filtering, alignment, barcode counting, transposase cut site identification, peak detection, and cell calling.
  • Automated Library Aggregation: Built-in support for combining multiple libraries with configurable normalization options (depth, signal, or none).
  • Quality Control Integration: Incorporates FastQC and MultiQC for comprehensive quality assessment and reporting.
  • Flexible Input Handling: Supports single, paired-end, and triple-read formats with automatic file format detection and processing.
  • GEO Dataset Compatibility: Specialized handling for GEO datasets with detailed instructions for proper file mapping.
  • Scalable Processing: Configurable CPU and memory allocation for optimal performance across different compute environments.

Input/Output Specification

Inputs

Required

FASTQ Reads Collection

  • Description: Triple collection of FASTQ files containing single-cell ATAC-seq reads (R1, R2, R3 for ATACv2 or R1, R2, I2 for ATACv1)
  • Format: .fastq.gz
  • Example File Path: /path/to/reads/sample_S1_L001_R1_001.fastq.gz

Reference Genome

  • Description: Cell Ranger ATAC compatible reference genome index
  • Format: Cell Ranger ATAC reference directory
  • Example File Path: /path/to/reference/refdata-cellranger-arc-GRCh38-2020-A-2.0.0

Outputs

Reported Outputs

  • Web Summary HTML:
  • Description: Interactive HTML report containing analysis summary, QC metrics, and visualizations
  • Format: .html
  • Example File Path: /output/sample/outs/web_summary.html
  • Visualization App: Web browser

  • Location: Output directory

  • Peak-Barcode Matrix:

  • Description: Filtered peak-barcode count matrix in Market Exchange format
  • Format: .mtx, .tsv
  • Example File Path: /output/sample/outs/filtered_peak_bc_matrix/
  • Visualization App: R/Python analysis tools, Loupe Browser

  • Location: Output directory

  • Fragments File:

  • Description: Compressed TSV file containing all observed fragments
  • Format: .tsv.gz
  • Example File Path: /output/sample/outs/fragments.tsv.gz
  • Visualization App: IGV, UCSC Genome Browser
  • Location: Output directory

Supporting Outputs

  • Single Cell CSV:
  • Description: Per-barcode metrics including cell classification and QC statistics
  • Format: .csv

  • Example File Path: /output/sample/outs/singlecell.csv

  • FastQC Reports:

  • Description: Quality control reports for input FASTQ files
  • Format: .html, .zip

  • Example File Path: /output/fastqc/sample_fastqc.html

  • MultiQC Report:

  • Description: Aggregated quality control summary across all samples
  • Format: .html
  • Example File Path: /output/multiqc_report.html

Associated Processes

References & Additional Documentation