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Salmon Summary Specifications

Process Details

  • Name: Salmon Summary
  • Process UUID: cwhXijPHw1FfveulMyl7PRu0kAufV3
  • Process Group: Misc.

Overview

This process merges Salmon quantification output files from multiple samples into consolidated summary tables for downstream analysis. It processes both gene-level and transcript-level (isoform) expression data, creating unified expression matrices that facilitate comparative analysis across samples.

This process is implemented in Perl.

Key Functionality

  • GTF Annotation Parsing: Extracts gene-transcript relationships from GTF annotation files to map between transcript IDs and gene IDs
  • Multi-sample Data Integration: Aggregates Salmon abundance estimates from multiple sample directories into unified expression matrices
  • Dual-level Expression Tables: Generates separate summary tables for both gene-level and transcript-level expression data
  • Multiple Quantification Metrics: Creates tables for both expected counts and TPM (Transcripts Per Million) values

Input/Output Specification

Inputs

Required Inputs

  • Output Directory

    • Description: Directory containing Salmon quantification results from multiple samples, with subdirectories named following the pattern "genes_salmon_[sample_name]"
    • Format: Directory

  • GTF File

    • Description: Gene annotation file in GTF format containing gene and transcript annotations used for mapping relationships between genes and transcripts
    • Format: GTF

Outputs

  • Output File
    • Description: Consolidated expression summary tables including genes_expression_expected_count.tsv, genes_expression_tpm.tsv, isoforms_expression_expected_count.tsv, and isoforms_expression_tpm.tsv
    • 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