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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




No version available



  • person_outline Alexander Dobin

Publication for Spliced Transcripts Alignment to a Reference

STAR citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

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

[…] bam). 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). Normalizatio […]


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
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 ma […]


Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

Sci Rep
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x
call_split See protocol

[…] Raw sequencing reads were first mapped to the rat genome using STAR 2.5.2a with the 2-PASS option. The resulting 2-PASS bam files were processed by rMATS for exon inclusion level differences between lean and obese groups at each time point. Both exon–exon junctio […]


“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”

BMC Infect Dis
PMCID: 5952419
PMID: 29764370
DOI: 10.1186/s12879-018-3127-4
call_split See protocol

[…] per 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 d […]


Altered lung biology of healthy never smokers following acute inhalation of E cigarettes

PMCID: 5950177
PMID: 29754582
DOI: 10.1186/s12931-018-0778-z
call_split See protocol

[…] 2 mRNA library prep. The data are publically available in the NCBI Gene Expression Omnibus (GEO accession number: GSE85121). Illumina HiSeq paired-end reads from NYGC RNA-Seq data were processed with STAR (2.3.1z13_r470) to align reads to the GRCh37/hg19 human reference genome and RefSeq gene definitions (2014–06-02). Gene expression quantification was performed using Cufflinks (2.2) against the R […]


CD82 hypomethylation is essential for tuberculosis pathogenesis via regulation of RUNX1 Rab5/22

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

[…] rom 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 was defined […]


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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.
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Anonymous user #12651

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Common use in targeted RNA-seq.

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