Skip to content

featureCounts Specifications

Process Details

  • Name: featureCounts
  • Process UUID: gvzzNcn5xY2EtoJum37rYemGqHERDx
  • Process Group: Transcript Quant.

Overview

featureCounts is 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. It can be used to count both RNA-seq and genomic DNA-seq reads. This process quantifies gene expression by counting the number of sequencing reads that map to each genomic feature, producing a count matrix essential for downstream differential expression analysis.

This process is implemented in Groovy/Nextflow, which invokes the featureCounts tool from the Subread package.

Key Functionality

  • Read Summarization: Counts mapped sequencing reads for genomic features defined in annotation files
  • Flexible Annotation Support: Accepts both GTF (Gene Transfer Format) and SAF (Simplified Annotation Format) files for feature definitions
  • Paired-end Compatibility: Automatically handles both single-end and paired-end sequencing data
  • Customizable Parameters: Supports user-defined parameters for fine-tuning counting behavior

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads

    • Description: BAM files containing aligned sequencing reads
    • Format: BAM

  • Mate Information

    • Description: Specifies whether the data is single-end or paired-end
    • Format: Mate parameter

  • Run Parameters

    • Description: Configuration parameters for the analysis run
    • Format: Run parameters

  • GTF File

    • Description: Gene annotation file in GTF format containing genomic feature coordinates
    • Format: GTF

Optional Inputs

  • SAF File
    • Description: Simplified annotation format file as an alternative to GTF for feature definitions
    • Format: SAF

Outputs

  • Feature Counts Table
    • Description: Tab-separated file containing read counts for each genomic feature
    • Format: TSV

References & Resources

  • Tool Documentation: Contact the team for details on featureCounts
  • 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. DOI: 10.1093/bioinformatics/btt656