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STAR specifications


Unique identifier OMICS_01254
Alternative name Spliced Transcripts Alignment to a Reference
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.5.4b
Stability Stable
Maintained Yes



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  • person_outline Alexander Dobin <>

Publication for Spliced Transcripts Alignment to a Reference

STAR in pipelines

PMCID: 5753437
PMID: 29298676
DOI: 10.1186/s12864-017-4411-1

[…] and aligned using the rna-seq pipeline described in []. in short, reads were filtered for ribosomal rna, trimmed and aligned to version 3 of the populus trichocarpa reference genome [–] with star []. the number of reads aligning to annotated gene models was determined using htseq []. read counts were normalized with a variance stabilizing transformation (vst) implemented in the r-package […]

PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] for host gene independent circrnas []. dcc 0.0.4 ( was used to quantify host gene read counts. in accordance with the dcc pipeline, fastq files were mapped with star 2.5 [] using the recommended parameters. picard 2.2.4 ( was used to remove duplicated reads from the bam files. the circrna raw read counts (using […]

PMCID: 5754050
PMID: 29300724
DOI: 10.1371/journal.pgen.1007127

[…] reference genome grcm38 (version m12, ensembl release 87) and the ercc reference sequence (thermo fisher) were combined and used as the reference genome for sequencing alignment, performed using star (version 2.4.2a) []. the expression levels of 49,585 features annotated in the gencode mouse genome and 92 ercc features were determined using htseq (version 0.6.1p1) []. the following […]

PMCID: 5764994
PMID: 29323241
DOI: 10.1038/s41598-017-19072-5

[…] reads were mapped against the reference pig genome (sscrofa10.2) and the annotation database ensembl genes 86 using the open-source software star 2.5.2a. mapping quality evaluation and descriptive statistics were generated with qualimap v.2.2. the resulting bam files containing the aligned sequences were subsequently merged with samtools. […]

PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] underwent quality control analysis using fastqc ( and the quality checked reads were then aligned to the human genome (assembly hg38) using star version 2.5.0a. differentially expressed transcripts (fold-change ≥ |1.5|, fdr ≤ 0.05) were identified as described., intron retention level (ir ratio) was computed for each sample using […]

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STAR in publications

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

[…] initial quality control of raw sequencing reads was done with fastqc (version 0.11.4) followed by pre-processing with prinseq-lite (version 0.20.4). resulting high-quality reads were mapped via star (version 2.5.0b) against the mouse (grcm38) reference genome. after processing of the alignment results with samtools (0.1.19) counts per gene were obtained by htseq (version 0.6.0). […]

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] ( using gene annotation files obtained from illumina ( rna-seq reads were also mapped using star with the proposed encode parameters and xenome on the human hg19 and mouse mm10 genomes and transcript annotation (ensembl 75). gene counts were normalized using reads per kilobase per million […]

PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] 3, we next performed an exon-level analysis of the rna-seq data to examine alternative splicing in an unbiased manner. raw sequence reads were mapped to the ensembl v87 annotated rat genome using star. to find as many novel junctions as possible, the star 2-pass protocol was used. the rmats package was then applied to discover both annotated and novel exons, and to calculate differences […]

PMCID: 5952419
PMID: 29764370
DOI: 10.1186/s12879-018-3127-4

[…] sample. quality check of reads was performed with the software fastqc. low quality reads and adapters were trimmed with cutadapt []. trimmed reads were mapped to the human genome grch38/hg19 with star [], and the expression level for each gene was counted with htseq [] according to gene annotations from ensembl. the bioconductor deseq package in r [] was used to normalize the counts and call […]

PMCID: 5951854
PMID: 29760437
DOI: 10.1038/s12276-018-0091-4

[…] rna-seq experiments were clipped and trimmed of adapters, and low-quality reads were removed using trimmomatic. quality-controlled fastq files were aligned to the ucsc hg19 reference genome using star (version 2.5.1) aligner software with three mismatches. to measure differential gene expression, deseq2 with the default parameters was used. a subset of condition-specific expression […]

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STAR institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Pacific Biosciences, Menlo Park, CA, USA
STAR funding source(s)
Supported by NHGRI (NIH) grant U54HG004557.

STAR reviews

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Sangram keshari sahu

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STAR do fast mapping compared to other sort read aligner tools (like TopHat2 and Hisat2). You can find lots of options to modify for desired output. Plus point with STAR aligner is - Along with SAM and BAM align output files it also gives RAW read count just like HTseq-count. So lot better insights without additional tools for conversion.

Antoine Rousselin

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Common use in targeted RNA-seq.

Very rich tool, still a lot of parameters to use and understand!