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featureCounts Prep Specifications

Process Details

  • Name: featureCounts Prep
  • Process UUID: HHqTaNQuaD9OOPeA54Q9Aked2857Jd
  • Process Group: Transcript Quant.

Overview

featureCounts Prep is a configuration process that prepares parameters for featureCounts, a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. This process sets up the necessary parameters and run configurations for both RNA-seq and genomic DNA-seq read counting workflows.

This process is implemented in Groovy.

Key Functionality

  • Parameter Configuration: Sets up featureCounts parameters for gene-level and transcript-level quantification
  • Strand-specific Analysis: Optionally configures sense and antisense strand quantification
  • Multi-run Setup: Generates multiple parameter sets for comprehensive expression analysis
  • Quality Control Settings: Configures mapping quality thresholds and overlap requirements

Input/Output Specification

Inputs

Required Inputs

  • run_featureCounts
    • Description: Control parameter to determine whether featureCounts should be executed
    • Format: String value ("yes" or "no")

Outputs

  • run_parameters
    • Description: Configured parameter sets for featureCounts execution, including run names and command-line parameters
    • Format: Structured parameter data

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Define each of the featureCounts Parameters

    • Description: prefix for run output
    • Default value: ["gene_id","transcript_id"]

  • featureCounts Parameters

    • Description: -s Indicate strand-specific read counting: 0 (unstranded, default), 1 (stranded) and 2 (reversely stranded) -Q The minimum mapping quality score -T Number of threads -B requireBothEndsMapped -C countChimericFragments --fracOverlap Minimum fraction of overlapping bases --minOverlap Minimum number of overlapping bases
    • Default value: ["-g gene_id -s 0 -Q 20 -T 2 -B -d 50 -D 1000 -C --fracOverlap 0 --minOverlap 1","-g transcript_id -s 0 -Q 20 -T 2 -B -d 50 -D 1000 -C --fracOverlap 0 --minOverlap 1"]

  • Quantify sense/antisense genes and transcripts

    • Description: Quantify sense/antisense genes and transcripts
    • Available options: Yes, No (default)

References & Resources

  • Tool Documentation: Contact the team for details on featureCounts configuration
  • Related Papers: Liao, Y., Smyth, G.K. and Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930.