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Salmon Alignment Summary Specifications

Process Details

  • Name: Salmon Alignment Summary
  • Process UUID: VhIQM6mJvG1agBJIWzDyca3gYzgrt9
  • Process Group: Misc.

Overview

This process aggregates Salmon alignment summary information from multiple samples into a unified tabular format. It extracts key alignment statistics from Salmon quantification output directories and compiles them into a comprehensive summary table for downstream analysis and quality assessment.

This process is implemented in Perl.

Key Functionality

  • Sample Detection: Automatically identifies all Salmon output directories with the prefix "salmon_" in the input directory
  • Statistics Extraction: Parses Salmon metadata files to extract total reads, pseudoaligned reads, and uniquely mapped reads for each sample
  • Data Aggregation: Compiles alignment statistics from all samples into a single tabular summary file
  • Quality Assessment: Provides alignment rate metrics to evaluate the success of the RNA-seq quantification process

Input/Output Specification

Inputs

Required Inputs

  • Output Directory
    • Description: Directory containing Salmon quantification output folders (named with "salmon_" prefix)
    • Format: Directory

Outputs

  • Alignment Summary Table
    • Description: Tab-separated file containing alignment statistics for all samples including total reads, pseudoaligned reads, and uniquely mapped reads
    • Format: TSV

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the Perl script implementation
  • Related Papers: Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14(4), 417-419. https://doi.org/10.1038/nmeth.4197