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Cellranger ARC count Specifications

Process Details

  • Name: Cellranger ARC count
  • Process UUID: f9315g2iup3t0dlmbu52kf2il0hhv2
  • Process Group: SingleCell

Overview

This process performs single-cell multimodal analysis by running Cell Ranger ARC count on paired gene expression and chromatin accessibility data. Cell Ranger ARC is designed to process single-cell RNA-seq and ATAC-seq data simultaneously from the same cells, enabling comprehensive analysis of gene expression and chromatin accessibility profiles.

This process is implemented in Bash, which orchestrates the Cell Ranger ARC pipeline for multimodal single-cell data processing.

Key Functionality

  • Multimodal Data Processing: Simultaneously processes single-cell RNA-seq (gene expression) and ATAC-seq (chromatin accessibility) data from the same experiment
  • FASTQ File Organization: Automatically organizes and concatenates FASTQ files by library type (Gene Expression and Chromatin Accessibility) into the required directory structure
  • Cell Barcode Matching: Matches cell barcodes across RNA and ATAC modalities to ensure proper pairing of measurements from the same cells
  • Feature-Barcode Matrix Generation: Produces both raw and filtered feature-barcode matrices containing gene expression and peak accessibility counts
  • Quality Control Reporting: Generates comprehensive web-based quality control reports with metrics for both modalities

Input/Output Specification

Inputs

Required Inputs

  • directory

    • Description: Directory containing FASTQ files organized by library type (Gene Expression and Chromatin Accessibility)
    • Format: Directory

  • reference

    • Description: Cell Ranger ARC-compatible reference genome with both transcriptome and ATAC-seq peak annotations
    • Format: Reference file (.ref)

Outputs

  • outputHTML

    • Description: Web summary report containing quality control metrics, cell calling statistics, and analysis results for both RNA and ATAC modalities
    • Format: HTML file

  • h5_file (raw)

    • Description: Raw feature-barcode matrix in HDF5 format containing unfiltered gene expression and peak accessibility counts for all detected barcodes
    • Format: H5 file

  • h5_file (filtered)

    • Description: Filtered feature-barcode matrix in HDF5 format containing gene expression and peak accessibility counts for high-quality cell barcodes only
    • Format: H5 file

  • directory

    • Description: Complete Cell Ranger ARC output directory containing all analysis results, including matrices, metrics, and intermediate files
    • Format: Directory

Parameters & Settings

This process uses default Cell Ranger ARC parameters optimized for standard multimodal single-cell experiments. Resource allocation is automatically managed based on available computational resources.

References & Resources

  • Tool Documentation: Cell Ranger ARC User Guide
  • Related Papers: Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.e29 (2021). DOI: 10.1016/j.cell.2021.04.048