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Cell Ranger ARC Pipeline Specification

Pipeline Details

  • Name: Cell Ranger ARC
  • Pipeline UUID: cb1fd236c5bf4d6783f4c1fbc69d56f5
  • Version: 1.0.3
  • View Pipeline:

Overview

Cell Ranger ARC pipeline is designed for analyzing Chromium Single Cell Multiome ATAC + Gene Expression sequencing data. It provides comprehensive analysis of gene expression and chromatin accessibility at a single cell level, automating data preprocessing, quality control, and downstream analysis to ensure reliable and reproducible results.

Key Use cases:

  • Single Cell Multiome Analysis: Simultaneous analysis of gene expression and chromatin accessibility from the same single cells.
  • Joint Gene Expression and ATAC-seq Processing: Integrated processing of RNA-seq and ATAC-seq data from multiome experiments.
  • Cell Type Identification: Discovery and characterization of cell types based on combined transcriptomic and epigenomic profiles.

Features

  • Multiome Data Processing: Specifically designed for 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression data.
  • Automated Directory Structure: Intelligently organizes FASTQ files into appropriate RNA and ATAC subdirectories based on library type.
  • Flexible Input Configuration: Supports both R1/R2 only configurations and R1/R2/I2 configurations depending on barcode placement.
  • Containerized Execution: Uses Cell Ranger ARC container (quay.io/viascientific/cellranger-arc:1.0.0) for consistent results.
  • Comprehensive Output Generation: Produces web summaries, feature-barcode matrices, and complete output directories.
  • Library Type Management: Automatically handles "Gene Expression" and "Chromatin Accessibility" library types from configuration files.

Input/Output Specification

Inputs

Required

FASTQ Files

  • Description: Raw sequencing reads from Chromium Single Cell Multiome ATAC + Gene Expression experiments. Files should be named with specific patterns ending in .R1.fastq.gz, .R2.fastq.gz, and optionally .R3.fastq.gz.
  • Format: .fastq.gz
  • Example File Path: /path/to/sample_name.R1.fastq.gz

Library Configuration File

  • Description: Tab-delimited file containing sample information with required columns for input_name, group, and library_type. Each sample requires two entries: one for "Gene Expression" and one for "Chromatin Accessibility".
  • Format: Tab-separated values (.tsv)
  • Required Columns: input_name, group, library_type
  • Example: 
    input_name  group   library_type
Sample_01   Group1  Gene Expression
Sample_01   Group1  Chromatin Accessibility

Reference Genome

  • Description: Cell Ranger ARC compatible reference genome for alignment and feature counting.
  • Format: Cell Ranger ARC reference directory
  • Example File Path: /path/to/refdata-cellranger-arc-GRCh38-2020-A-2.0.0

Outputs

Reported Outputs

  • Web Summary HTML:
  • Description: Interactive HTML report containing quality metrics, cell counts, and analysis summaries
  • Format: .html
  • Example File Path: /output/directory/sample_web_summary.html
  • Visualization App: Web browser

  • Location: Output folder

  • Raw Feature Barcode Matrix:

  • Description: HDF5 file containing unfiltered feature-barcode matrix with all detected barcodes
  • Format: .h5
  • Example File Path: /output/directory/sample_raw_feature_bc_matrix.h5
  • Visualization App: R/Python analysis tools

  • Location: Output folder

  • Filtered Feature Barcode Matrix:

  • Description: HDF5 file containing filtered feature-barcode matrix with only cell-associated barcodes
  • Format: .h5
  • Example File Path: /output/directory/sample_filtered_feature_bc_matrix.h5
  • Visualization App: R/Python analysis tools, Loupe Browser
  • Location: Output folder

Supporting Outputs

  • Complete Output Directory:
  • Description: Full Cell Ranger ARC output directory containing all analysis results, BAM files, and intermediate files
  • Format: Directory structure
  • Example File Path: /output/directory/sample_outs/
  • Location: Output folder

Associated Processes

References & Additional Documentation