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Salmon Transcript To Gene Count Specifications

Process Details

  • Name: Salmon Transcript To Gene Count
  • Process UUID: A3p3GUDzcqJk1AcT6L1GnDHrVSVM81
  • Process Group: Misc.

Overview

This process converts Salmon transcript-level quantification output to gene-level count tables by aggregating transcript abundances to their corresponding genes. The process parses a GTF annotation file to map transcript IDs to gene IDs, then sums the transcript-level TPM (Transcripts Per Million) values to generate gene-level expression estimates.

This process is implemented in Bash, which invokes a Perl script for transcript-to-gene aggregation and file processing.

Key Functionality

  • GTF Parsing: Extracts transcript-to-gene ID mappings from GTF annotation files
  • Expression Aggregation: Sums transcript-level TPM values to calculate gene-level expression
  • Length Calculation: Determines representative gene lengths using the maximum transcript length per gene
  • ERCC Spike-in Handling: Preserves ERCC spike-in controls as separate entries in the output

Input/Output Specification

Inputs

Required Inputs

  • outputDir

    • Description: Directory containing Salmon transcript quantification results, specifically the abundance_isoforms.tsv file
    • Format: directory

  • gtfFile

    • Description: Gene annotation file in GTF format containing transcript-to-gene ID mappings
    • Format: gtf

Outputs

  • outputDir
    • Description: Output directory containing the gene-level abundance table (abundance_genes.tsv) with aggregated expression values
    • Format: directory

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 aggregation script