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Cell Ranger Count Specifications

Process Details

  • Name: Cell Ranger Count
  • Process UUID: UjR58kcIVY9wpE6jCHBARoNa6ZOG9s
  • Process Group: SingleCell

Overview

Cell Ranger Count is a comprehensive single-cell RNA sequencing analysis process that processes FASTQ files to generate feature-barcode matrices and perform gene expression analysis. The process performs alignment, filtering, barcode counting, and UMI counting using Chromium cellular barcodes to determine clusters and analyze gene expression patterns. It also supports Feature Barcoding data processing alongside standard Gene Expression reads.

This process is implemented in Bash, which invokes Cell Ranger software for single-cell RNA-seq data processing.

Key Functionality

  • Read Processing: Handles both single-end and paired-end FASTQ files with automatic compression detection and formatting
  • Barcode Analysis: Uses Chromium cellular barcodes to generate feature-barcode matrices and perform UMI counting
  • Gene Expression Analysis: Performs comprehensive gene expression analysis including clustering and cell type identification
  • Feature Barcoding Support: Processes Feature Barcoding data alongside standard Gene Expression reads
  • Quality Control: Generates comprehensive quality control metrics and web-based summary reports

Input/Output Specification

Inputs

Required Inputs

  • Sequencing Reads

    • Description: FASTQ files containing single-cell RNA-seq reads
    • Format: FASTQ (compressed or uncompressed)

  • Read Configuration

    • Description: Specifies whether reads are single-end or paired-end
    • Format: Configuration parameter

  • Reference Genome

    • Description: Cell Ranger-compatible reference transcriptome for alignment
    • Format: Cell Ranger reference directory

Outputs

  • Analysis Directory

    • Description: Complete Cell Ranger output directory containing all analysis results
    • Format: Directory structure

  • Web Summary Report

    • Description: Interactive HTML report with quality metrics and analysis summary
    • Format: HTML

  • Filtered Feature Matrix

    • Description: Filtered feature-barcode matrix containing high-quality cells
    • Format: HDF5

  • Raw Feature Matrix

    • Description: Unfiltered feature-barcode matrix containing all detected barcodes
    • Format: HDF5

  • Aligned Reads

    • Description: Position-sorted BAM file with aligned reads
    • Format: BAM

  • Raw Feature Directory

    • Description: Directory containing raw feature-barcode matrix files
    • Format: Directory with matrix files

References & Resources

  • Tool Documentation: Contact the team for details on Cell Ranger count pipeline
  • Related Papers: Zheng, G.X.Y., Terry, J.M., Belgrader, P. et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8, 14049 (2017). https://doi.org/10.1038/ncomms14049