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Cell Ranger VDJ Specifications

Process Details

  • Name: Cell Ranger VDJ
  • Process UUID: c6638gzjl86xqzd948rlycqx4x3mwc
  • Process Group: SingleCell

Overview

Cell Ranger VDJ is a single-cell analysis process that takes FASTQ files from V(D)J libraries and performs sequence assembly and paired clonotype calling. This process is essential for analyzing T-cell and B-cell receptor sequences in single-cell RNA sequencing experiments, enabling the identification and characterization of immune cell clonotypes.

This process is implemented in Bash, which invokes the Cell Ranger VDJ pipeline for V(D)J sequence analysis.

Key Functionality

  • V(D)J Sequence Assembly: Assembles V(D)J sequences from single-cell FASTQ data to reconstruct full-length receptor sequences
  • Clonotype Calling: Identifies and calls paired clonotypes from assembled V(D)J sequences
  • Quality Control: Generates comprehensive quality metrics and web-based summary reports for V(D)J analysis results

Input/Output Specification

Inputs

Required Inputs

  • FASTQ Reads

    • Description: Set of FASTQ files containing V(D)J library sequencing data
    • Format: FASTQ files (paired-end)

  • Mate Information

    • Description: Specification of read pairing configuration
    • Format: Mate specification value

  • Reference

    • Description: V(D)J reference genome directory containing gene annotations and sequences
    • Format: Directory containing reference files

Outputs

  • Output Directory

    • Description: Complete Cell Ranger VDJ output directory containing all analysis results including clonotype calls and assembled sequences
    • Format: Directory

  • Web Summary Report

    • Description: Interactive HTML report summarizing V(D)J analysis results, quality metrics, and clonotype statistics
    • Format: HTML file

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Sample ID
    • Description: (optional) Id of the sample
    • Default value: (uses sample name if not specified)

References & Resources

  • Tool Documentation: Contact the team for details on Cell Ranger VDJ pipeline
  • Related Papers: Zheng, G.X., 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