Skip to content

Kallisto Transcript To Gene Count Specifications

Process Details

  • Name: Kallisto Transcript To Gene Count
  • Process UUID: fyx8lDB3b2ZySi7RkgQ0z4Td8XaBzE
  • Process Group: Misc.

Overview

This process converts Kallisto transcript-level quantification output to gene-level count tables by aggregating transcript expression values to their corresponding genes. The process uses GTF annotation files to map transcript IDs to gene IDs and sums the expression values (TPM) for all transcripts belonging to the same gene.

This process is implemented in Perl.

Key Functionality

  • Transcript-to-Gene Mapping: Parses GTF annotation files to establish relationships between transcript IDs and gene IDs
  • Expression Aggregation: Sums transcript-level TPM values to generate gene-level expression estimates
  • Length Calculation: Determines representative gene lengths by selecting the maximum length among constituent transcripts
  • ERCC Spike-in Handling: Preserves External RNA Controls Consortium (ERCC) spike-in controls in the output

Input/Output Specification

Inputs

Required Inputs

  • outputDir

    • Description: Directory containing Kallisto transcript quantification results with abundance_isoforms.tsv file
    • Format: directory

  • gtfFile

    • Description: Gene Transfer Format annotation file containing transcript-to-gene 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 conversion script