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Cellranger Multi Specifications

Process Details

  • Name: cellranger_multi
  • Process UUID: WHinNg0Gq139SvwwCnd6zIgty0OD6r
  • Process Group: SingleCell

Overview

This process generates a Cell Ranger multi configuration file and executes the Cell Ranger multi pipeline for comprehensive single-cell RNA sequencing analysis. It handles multiple data types including gene expression, feature barcoding (CITE-seq, cell hashing), and V(D)J immune profiling in a unified workflow. The process automatically configures library information, sample demultiplexing parameters, and reference data based on the provided inputs.

This process is implemented in Bash, which invokes a Python script for configuration file generation and Cell Ranger multi command execution.

Key Functionality

  • Configuration File Generation: Creates a comprehensive Cell Ranger multi CSV configuration file with gene expression, feature barcoding, and V(D)J sections
  • Multi-Modal Analysis: Processes gene expression, feature barcoding (CMO, hashtag, probe barcodes), and V(D)J immune receptor data simultaneously
  • Sample Demultiplexing: Handles cell multiplexing and demultiplexing using various barcoding strategies
  • Quality Control: Generates web summary reports and filtered results for each sample
  • Output Organization: Automatically organizes results into sample-specific directories with standardized naming

Input/Output Specification

Inputs

Required Inputs

  • reference

    • Description: Cell Ranger compatible reference genome directory containing transcriptome and genome annotations
    • Format: directory

  • csvFile

    • Description: Sample configuration file containing library and sample metadata
    • Format: csv

  • settings

    • Description: Analysis parameters and configuration settings for Cell Ranger multi
    • Format: settings

Optional Inputs

  • reads

    • Description: FASTQ files containing sequencing reads from single-cell libraries
    • Format: fastq

  • feature_reference

    • Description: Feature reference file defining antibody or guide RNA sequences for feature barcoding
    • Format: csv

  • VDJ_reference

    • Description: V(D)J reference sequences for immune receptor analysis
    • Format: csv

  • bcl_directory

    • Description: Base call files directory for demultiplexing from sequencer output
    • Format: bcl_directory

  • cmo_set

    • Description: Cell Multiplexing Oligo (CMO) reference file for sample demultiplexing
    • Format: csv

Outputs

  • outputDir

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

  • outputHTML

    • Description: Web summary report with quality metrics and analysis results
    • Format: html

  • csvFile

    • Description: Generated configuration files and filtered annotation results
    • Format: csv

References & Resources

  • Tool Documentation: Contact the team for details on the Cell Ranger multi Python configuration script
  • 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