Subread protocols

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chevron_left Gene fusion detection Read alignment Alternative splicing events identification Known transcript quantification Spliced read alignment Table of counts Variant detection chevron_right
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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



Add your version



  • person_outline Wei Shi <>

Additional information

An R version is available at:

Publications for Subread

Subread in pipelines

PMCID: 5766599
PMID: 29330370
DOI: 10.1038/s41598-017-18407-6

[…] redundant mapping at the same locus for both genome and transcriptome was consolidated as one single hit. the read count for each annotated transcript was then derived from mapped reads by rsubread. some of the key statistics of read mapping is shown on table .table 1, a heatmap generated from expression of differentially expressed lncrnas detected by edger on three pairs of matched […]

PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] reference genomes of three acidophiles, including the newly assembled chromosome of l. ferriphilumt, with bowtie2 v2.3.2 with default settings. read mappings to cdss were counted with the software featurecounts from subread package v1.5.2 (), and the −s 2 option was used to include only reads on the correct strand. raw read counts were normalized to the gene length and the sum of total counted […]

PMCID: 5785820
PMID: 29416570
DOI: 10.1186/s13148-018-0446-7

[…] and the converted dna was amplified by pcr and sequenced on a hiseq2500 illumina instrument as 50 bp single end reads, and processed by casava 1.8.2., srna reads were aligned to hg19 using the subread aligner using the recommended settings for mirna mapping with the exception that only uniquely mapping reads were kept []. unmapped reads were aligned first ribosomal sequences allowing […]

PMCID: 5799263
PMID: 29403061
DOI: 10.1038/s41598-018-20885-1

[…] motor (servo motor), or static cultured condition (st) for 24 hours (n = 4, respectively). rna-seq fastq files were aligned to the current version of the human genome primary assembly using the subread program and the gencode v24 annotation was used for summarizing read counts on each gene. the limma package along with the voom transformation was used for differential expression analysis […]

PMCID: 5852087
PMID: 29540736
DOI: 10.1038/s41598-018-22617-x

[…] option for meta samples. reads were mapped to the meta-transcriptome with bowtie2 v2.0.6 using default settings. bam files were converted with samtools v0.1.18, and gene coverage was calculated with subread version 1.4.6., the proteins were annotated with kaas, with sbh and ghostx as settings and with interproscan 5.6-48.0. the annotation was further enhanced by adding ec numbers via priam […]

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Subread in publications

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 […]

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 […]

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 […]

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 […]

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, […]

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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.