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Subread specifications


Unique identifier OMICS_01255
Name Subread
Alternative name Rsubread
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.2
Stability Stable
Maintained Yes


  • align
  • buildIndex
  • exactSNP
  • featureCounts
  • propmappe
  • Subindel
  • Subjunc
  • Sublong




No version available



  • person_outline Wei Shi

Additional information

An R version is available at:

Publications for Subread

Subread citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] as measured by microarray analysis. igv was used for manual inspection and visualization of data. for the analysis of histone mark intensities in genes, mapped reads per gene were counted with featurecounts (1.5.0), respective input counts subtracted, and normalized via tmm using the edger package. the pearson correlation coefficient between changes in respective histone marks over gene […]


Elucidating the genetic architecture of reproductive ageing in the Japanese population

Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] then aligned to the rn6 build of the rat genome with bowtie2/tophat2, using default parameters. aligned reads were assigned to gene-level genomic features of the ensembl 83 annotation set using the rsubread featurecounts r function with countmultimappingreads and allowmultipleoverlaps flags set to true. differential expression between time points was then analysed using the generalized linear […]


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] aligner. low-quality reads (mapping quality <20) as well as known adapter contaminations were filtered out using cutadapt (version 1.10.0). read counting was performed using bioconductor packages rsubread and differential expression analysis with edger,. the conditions were contrasted against the growing samples. genes were identified as differentially expressed with a fdr (false discovery […]


Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer

Sci Rep
PMCID: 5940817
PMID: 29740154
DOI: 10.1038/s41598-018-25516-3

[…] ncbi genome information: ncbi genome/82 (bos taurus)) using the tophat aligner version 2.0.14 ( the reads mapped to each gene were counted using the featurecounts tool. differential expression analysis was performed using the edger package by pairwise comparisons between experimental groups. multiple testing correction was performed using edger […]


Limited utility of tissue micro arrays in detecting intra tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer

J Transl Med
PMCID: 5941467
PMID: 29739401
DOI: 10.1186/s12967-018-1495-6

[…] 0.05–alignsjdboverhangmin 1–alignsjoverhangmin 8–alignintronmax 1,000,000–alignmatesgapmax 1,000,000–outfiltermultimapnmax 50”., gene expression values were computed with the function featurecounts from the r package rsubread., differential expression was computed using the generalized linear model implemented in the bioconductor package edger. in the statistical model, […]


Optimizing exosomal RNA isolation for RNA Seq analyses of archival sera specimens

PLoS One
PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913

[…] to version hg38 of the human genome reference sequence using star []. mapped reads were then matched to genomic features (i.e. mrnas and lncrnas) annotated in gencode25 [] and ercc annotations using rsubread package, version 1.24.0 [], to generate raw counts for each gene. raw read count data were normalized to ercc spike-in values across samples using bioconductor package ruvseq_1.8.0 []. […]

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Subread institution(s)
Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
Subread funding source(s)
Supported by the Project Grant [1023454] and a Fellowship from the Australian National Health and Medical Research Council (NHMRC); Victorian State Government Operational Infrastructure Support; Australian Government [NHMRC IRIIS].

Subread reviews

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Arup Ghosh

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Very fast and easy to use tool for extracting raw read counts from aligned files. This tool can take multiple aligned files together and combines the output in one file for further analysis.


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Easy to use. I routinely use featureCounts for RNA-Seq data it is much faster than HTSeq-count for generating read counts.