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Cellranger Multi Prep Specifications

Process Details

  • Name: cellranger_multi_prep
  • Process UUID: jqMxOUvnFYSQsDu1ArbcZRha9edatr
  • Process Group: SingleCell

Overview

This process prepares for the execution of the "cellranger multi" command by grouping configuration files based on the provided lanes and lane of samples. It creates separate configuration files for each unique lane, enabling efficient batch processing of single-cell RNA sequencing data with Cell Ranger.

This process is implemented in Groovy, which invokes a Python script for configuration file generation and lane grouping.

Key Functionality

  • Configuration File Grouping: Groups library configuration files based on unique lanes and sample lanes
  • Multi-Sample Processing: Handles multiplexed single-cell samples with various barcode types (CMO, hashtag, OCM, probe)
  • Parameter Validation: Processes and validates Cell Ranger multi parameters for gene expression, feature barcode, and VDJ libraries

Input/Output Specification

Inputs

Required Inputs

  • librarySettings
    • Description: Configuration settings containing library information, sample groupings, and processing parameters
    • Format: librarySettings

Outputs

  • csvFile

    • Description: Generated CSV configuration files for each unique lane group
    • Format: csv

  • settings

    • Description: Processed settings object containing all validated parameters for downstream Cell Ranger multi execution
    • Format: settings

Parameters & Settings

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

  • Sample Separation (Optional – Only necessary when using multiplexed reactions)

    • Description: A name to identify a multiplexed sample. Must be alphanumeric with hyphens and/or underscores, and less than 64 characters. Required for cell multiplexing libraries.
    • Default value: ""

  • Group

    • Description: Use this column to run Cell Ranger Multi separately for different groups of samples. Samples that share the same group value will be grouped together and processed together.
    • Default value: ""

  • CMO IDs

    • Description: Required for 3' cell multiplexing libraries. The cell multiplexing oligo IDs used to multiplex this sample. If multiple CMOs were used per sample, separate IDs with a pipe (e.g., CMO301|CMO302).
    • Default value: ""

  • Hashtag IDs

    • Description: Required for 'Cell or sample hashing with Antibody Capture' libraries. The hashtag IDs used to multiplex this sample. If multiple antibody hashtags were used for the same sample, you can separate IDs with a pipe (e.g., ABHT-1| ABHT-2)
    • Default value: ""

  • OCM Barcode IDs

    • Description: Required for 3' and 5' GEM-X On-chip multiplexing (OCM) libraries. The OCM barcode IDs used to multiplex this sample. Must be one of OB1, OB2, OB3, OB4. If multiple OCM Barcodes were used for the same sample, you can separate IDs with a pipe (e.g., OB1|OB2)
    • Default value: ""

  • Probe Barcode IDs

    • Description: Required for FLEX libraries. The Fixed RNA Probe Barcode IDs, Antibody Multiplexing Barcode IDs, and CRISPR Multiplexing Barcode IDs used in the experiment.
    • Default value: ""

  • Description

    • Description: Optional. A description for the sample.
    • Default value: ""

  • Create BAM

    • Description: Setting the option to false reduces the overall computation time and decreases the size of the output directory, as it omits the generation of the BAM file Default: TRUE
    • Available options: TRUE (default), FALSE

  • Expected Cells

    • Description: Optional, recommended. Expected number of recovered cells.
    • Default value: ""

  • Force Cells

    • Description: Optional, Force pipeline to use this number of cells, bypassing cell detection. Default: detect cells using Cell Rangers cell calling algorithm.
    • Default value: ""

  • Chemistry

    • Description: Assay configuration. You should only specify chemistry if there is an error in automatic detection. Select one of: auto for autodetection (default),threeprime for Single Cell 3',SC3Pv1 or SC3Pv2 or SC3Pv3 for Single Cell 3' v1/v2/v3, SC3Pv3HT for Single Cell 3' v3.1 HT, SC-FB for Single Cell Antibody-only 3' v2, fiveprime for Single Cell 5', SC5P-PE for paired-end or SC5P-R2 for R2-only, SC-FB for Single Cell Antibody-only.
    • Available options: auto (default), threeprime, fiveprime, SC5P-PE, SC5P-R2, SC3Pv1, SC3Pv2, SC3Pv3, SC3Pv3HT, SC-FB, ARC-v1

  • R1 Length

    • Description: Optional. Hard trim the input Read 1 of gene expression libraries to this length before analysis.
    • Default value: ""

  • Check Library Compatibility

    • Description: Optional.This option allows users to disable the check that evaluates 10x Barcode overlap between libraries when multiple libraries are specified (e.g., Gene Expression + Antibody Capture). Setting this option to false will disable the check across all library combinations. We recommend running this check (default), however if the pipeline errors out, users can bypass the check to generate outputs for troubleshooting
    • Available options: TRUE (default), FALSE

  • Include Introns

    • Description: Optional. Including introns in analysis is recommended to maximize sensitivity. Default: TRUE
    • Available options: TRUE (default), FALSE

  • R1 Length Feature

    • Description: Optional. Hard trim the input Read 1 of Feature Barcode libraries to this length before analysis.
    • Default value: ""

  • R1 Length VDJ

    • Description: Optional. Hard trim the input Read 1 of Vdj libraries to this length before analysis. Default: do not trim Read 1.
    • Default value: ""

References & Resources

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