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Kallisto Summary Specifications

Process Details

  • Name: Kallisto Summary
  • Process UUID: iDWNKEScsoxhwDJiwSMGY0UzF46smV
  • Process Group: Misc.

Overview

This process merges Kallisto output files into a single comprehensive table file. It processes the quantification results from multiple Kallisto runs and combines them into unified expression matrices for downstream analysis. The process creates separate output files for both gene-level and transcript-level expression data, with both expected counts and TPM (Transcripts Per Million) values.

This process is implemented in Perl.

Key Functionality

  • GTF File Parsing: Extracts gene-to-transcript and transcript-to-gene mappings from the provided GTF annotation file
  • Kallisto Output Integration: Merges abundance files from multiple Kallisto quantification runs into unified expression matrices
  • Multi-level Expression Tables: Generates separate tables for gene-level and transcript-level expression data with both expected counts and TPM values

Input/Output Specification

Inputs

Required Inputs

  • Output Directory

    • Description: Directory containing Kallisto quantification results from multiple samples, with subdirectories named in the format "genes_kallisto_[sample_name]"
    • Format: Directory

  • GTF File

    • Description: Gene Transfer Format annotation file containing gene and transcript annotations for mapping between gene IDs and transcript IDs
    • Format: GTF

Outputs

  • Output Files
    • Description: Four tab-separated value files containing merged expression data: 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 Kallisto summary Perl script