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Ambient RNA QC Specifications

Process Details

  • Name: Ambient RNA QC
  • Process UUID: 417hes89wndtbsqln2p6s8it5okv84
  • Process Group: SingleCell

Overview

This process estimates the abundance of ambient RNA and generates a corrected count matrix using deconX. Ambient RNA contamination is a common issue in single-cell RNA sequencing where RNA from lysed or damaged cells contaminates the droplets containing intact cells, leading to artificially inflated gene expression profiles. This process identifies and removes ambient RNA contamination to improve data quality for downstream single-cell analyses.

This process is implemented in Perl, which generates an R Markdown report and invokes R scripts for ambient RNA detection and removal using the deconX algorithm from the celda package.

Key Functionality

  • Ambient RNA Detection: Uses deconX algorithm to identify ambient RNA contamination by comparing raw and filtered count matrices
  • Contamination Visualization: Generates plots showing the level of contamination across cells
  • Count Matrix Correction: Produces a corrected count matrix with ambient RNA removed (optional)
  • Quality Control Report: Creates an HTML report documenting the ambient RNA analysis and contamination levels

Input/Output Specification

Inputs

Required Inputs

  • Raw Count Matrix

    • Description: Raw feature-barcode matrix containing all droplets including empty ones
    • Format: H5 format

  • Filtered Count Matrix

    • Description: Filtered feature-barcode matrix containing only cell-containing droplets
    • Format: H5 format

Outputs

  • Corrected Count Matrix

    • Description: Count matrix with ambient RNA contamination removed (if correction is enabled)
    • Format: H5 format

  • Quality Control Report

    • Description: HTML report containing ambient RNA analysis results, contamination plots, and processing details
    • Format: HTML format

Parameters & Settings

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

  • Ambient RNA Removal
    • Description: Whether to generate a corrected count matrix with ambient RNA removed
    • Available options: yes, no (default)

References & Resources

  • Tool Documentation: Contact the team for details on the R Markdown script and deconX implementation
  • Related Papers: Yang, S., Corbett, S. E., Koga, Y., Wang, Z., Johnson, W. E., Yajima, M., & Campbell, J. D. (2020). Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biology, 21(1), 57. https://doi.org/10.1186/s13059-020-1950-6