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FeatureCounts

FeatureCounts

featureCounts is a tool to quantify RNA-seq and gDNA-seq data as counts. It is also suitable for single-cell RNA-seq (scRNA-seq) data. It supports multi-threading. The featureCounts is part of the Subread package (see links). An R version is also available as Rsubread .

Topic

Transcriptomics; Gene expression; RNA-seq

Details

  • Operation: Read summarisation
  • Input: FASTA, TXT
  • Output: BAM
  • Software interface: Command-line user interface
  • Language: C
  • Operating system: Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 2.0.0
  • Maturity: Mature
  • Credit: the Australian National Health and Medical Research Council (NHMRC), Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIIS.
  • Contact: Wei Shi shi _at_ wehi.edu.au | Yang Liao liao _at_ wehi.edu.au | Gordon K. Smyth smyth _at_ wehi.edu.au
  • Collection: Subread

Publications

Liao Y, Smyth GK, Shi W "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features." Bioinformatics. 2014 Apr 1;30(7):923-30. 2013 Nov 13. https://doi.org/10.1093/bioinformatics/btt656
PMID: 24227677


Liao Y, Smyth GK, Shi W "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote." Nucleic Acids Res. 2013 May 1;41(10):e108. 4. https://doi.org/10.1093/nar/gkt214
PMID: 23558742
PMCID: PMC3664803


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