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Cell Ranger ATAC Aggr Specifications

Process Details

  • Name: Cell Ranger ATAC Aggr
  • Process UUID: 2UTtHYPRORNY5GqEZyIFaKtCAcN2i5
  • Process Group: SingleCell

Overview

Cell Ranger ATAC Aggr aggregates multiple single-cell ATAC-seq libraries into a single analysis. The process takes a CSV file specifying cellranger-atac count output files (fragments.tsv.gz and singlecell.csv from each run) and produces a unified peak-barcode matrix containing all the combined data. This enables joint analysis of multiple ATAC-seq libraries with optional normalization to account for differences in sequencing depth or signal between samples.

This process is implemented in Bash, which invokes Cell Ranger ATAC for library aggregation and analysis.

Key Functionality

  • Library Aggregation: Combines multiple ATAC-seq libraries into a single analysis matrix
  • Depth Normalization: Applies optional normalization methods to account for sequencing depth differences between libraries
  • Dimensionality Reduction: Performs clustering and visualization using configurable dimensionality reduction methods
  • Quality Control: Generates comprehensive web summary reports for aggregated results

Input/Output Specification

Inputs

Required Inputs

  • outputDir

    • Description: Output directory for aggregated results
    • Format: Directory

  • reference

    • Description: Cell Ranger ATAC compatible reference genome directory
    • Format: Directory

Outputs

  • outputDir

    • Description: Complete Cell Ranger ATAC aggregation output directory containing peak-barcode matrices, analysis results, and metadata
    • Format: Directory

  • outputHTML

    • Description: Web summary report providing quality metrics and analysis overview for the aggregated libraries
    • Format: HTML

Parameters & Settings

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

  • A unique run ID string

    • Description: A unique run ID string: e.g. AGG123
    • Default value: aggr_libraries

  • Normalization Method

    • Description: String specifying how to normalize the input libraries. Valid values: depth (default), signal, or none
    • Available options: depth (default), signal, none

  • Skip Secondary Analysis

    • Description: Choose yes to skip secondary analysis which includes dimensionality reduction, clustering and visualization. This is applicable if you plan to use cellranger-atac reanalyze or your own custom analysis.
    • Available options: no (default), yes

  • Dimensionality Reduction Mode

    • Description: Dimensionality reduction mode for clustering. Valid values: lsa (default), pca, or plsa.
    • Available options: lsa (default), pca, plsa

References & Resources

  • Tool Documentation: Cell Ranger ATAC Documentation
  • Related Papers: Satpathy, A.T., Granja, J.M., Yost, K.E. et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 37, 925–936 (2019). https://doi.org/10.1038/s41587-019-0206-z