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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Open accessAbstract
MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. RESULTS: We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. AVAILABILITY AND IMPLEMENTATION: featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
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“Raw read counts are assembled outside limma using tools such as featureCounts (29), HTSeq-counts (30) or RSEM (31).”
From limma powers differential expression analyses for RNA-sequencing and microarray studies (2015) · cites this paper as [29]
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Metadata
- Authors
- Liao, Y., Smyth, G. K., & Shi, W.
- Affiliations
- The University of Melbourne (AU)
- Corresponding author
- Shi, Wei
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-13
- Volume
- 30
- Issue
- 7
- Pages
- 923-930
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2138207763
- Cited by
- 27,219
- References
- 47
- Citations by year
- 2026: 3661 · 2025: 4344 · 2024: 4323 · 2023: 3554 · 2022: 3316 · 2021: 2761 · 2020: 2083 · 2019: 1326 · 2018: 894 · 2017: 561 · 2016: 250 · 2015: 99 · 2014: 31 · 2013: 6
- FWCI
- 58.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- Australian Government
- Medical Research Council
- National Health and Medical Research Council (1023454)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- featureCounts, read counting, genomic features, paired-end reads, RNA-seq
- MeSH terms
- Algorithms, Histones, Software, Genome, Sequence Analysis, RNA, Genomics, High-Throughput Nucleotide Sequencing
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