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Cell Ranger ATAC Count Specifications

Process Details

  • Name: Cell Ranger ATAC Count
  • Process UUID: zwg48iZEYjG9U3h9gNwIm1xlyxsRTv
  • Process Group: SingleCell

Overview

Cell Ranger ATAC Count processes FASTQ files to perform comprehensive single-cell ATAC-seq analysis. This process takes FASTQ files from cellranger-atac mkfastq and performs complete ATAC analysis including read filtering and alignment, barcode counting, identification of transposase cut sites, detection of accessible chromatin peaks, cell calling, count matrix generation for peaks and transcription factors, dimensionality reduction, cell clustering, and cluster differential accessibility analysis.

This process is implemented in Groovy, which invokes Cell Ranger ATAC software for single-cell chromatin accessibility analysis.

Key Functionality

  • Read Processing: Filters and aligns FASTQ reads with proper barcode assignment
  • Peak Detection: Identifies accessible chromatin peaks and transposase cut sites
  • Cell Calling: Determines valid cell barcodes and generates count matrices
  • Dimensionality Reduction: Performs clustering and differential accessibility analysis

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: FASTQ files containing single-cell ATAC-seq sequencing data
    • Format: FASTQ files following naming convention [Sample Name]S1_L00[Lane Number][Read Type]_001.fastq.gz

  • Mate

    • Description: Sequencing configuration specifying read structure (single, pair, or triple)
    • Format: String value

  • Reference

    • Description: Cell Ranger ATAC reference genome directory
    • Format: Directory containing indexed reference genome

Outputs

  • Output Directory

    • Description: Complete Cell Ranger ATAC analysis results including count matrices, peaks, and analysis files
    • Format: Directory

  • Output HTML

    • Description: Web summary report containing quality metrics and analysis visualizations
    • Format: HTML file

Parameters & Settings

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

  • Run ID

    • Description: (optional) Id of the sample
    • Default value: (empty, uses sample name if not provided)

  • Force Cells

    • Description: (optional) Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger ATAC is not consistent with the barcode rank plot.
    • Default value: (empty)

  • Dimensionality Reduction

    • Description: (optional) Chose the algorithm for dimensionality reduction prior to clustering and tsne: 'lsa' (default), 'plsa', or 'pca'
    • Default value: (empty, defaults to lsa)

  • Downsample

    • Description: (optional) Force pipeline to downsample sequencing data to this number of gigabases.
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on Cell Ranger ATAC software
  • 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