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featureCounts summary Specifications

Process Details

  • Name: featureCounts_summary
  • Process UUID: 17fc63b6-e169-11e9-be30-e0aab38271b1
  • Process Group: Summary

Overview

This process merges featureCounts output files into single consolidated tables, providing a unified view of read count data across multiple samples. It processes both the count data and summary statistics from featureCounts analysis, creating comprehensive tables that facilitate downstream analysis and quality assessment.

This process is implemented in Perl.

Key Functionality

  • Count File Merging: Combines individual featureCounts output files from multiple samples into a single count matrix
  • Summary Statistics Consolidation: Merges featureCounts summary files containing alignment and counting statistics
  • Flexible Feature Support: Handles both gene-level and transcript-level counting data based on run configuration

Input/Output Specification

Inputs

Required Inputs

  • outputFileTSV
    • Description: featureCounts output files in TSV format containing read count data
    • Format: TSV

Outputs

  • outputFile

    • Description: Merged count matrix containing read counts for all features across samples
    • Format: TSV

  • outFileTSV

    • Description: Consolidated summary statistics from featureCounts analysis
    • 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 merging script