STAR protocols

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: 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) [90]. 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) [91]. 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 2.5.2a51. mapping quality evaluation and descriptive statistics were generated with qualimap v.2.252. the resulting bam files containing the aligned sequences were subsequently merged […]

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 2.5.0a47. differentially expressed transcripts (fold-change ≥ |1.5|, fdr ≤ 0.05) were identified as described48., intron retention level (ir ratio) was computed for each sample using […]

PMCID: 5778122
PMID: 29403501
DOI: 10.3389/fimmu.2018.00022

[…] trimmed of adapters, and the low-quality reads were removed by the trimmomatic (30). quality controlled fastq files were aligned to mus musculus ucsc mm10 reference genome sequence using the star (version 2.5.1) aligner software (31). to measure differential gene expression, deseq2 (32) with the default parameters was used. the rna-seq experiments were visualized using homer (33) […]

PMCID: 5778647
PMID: 29357872
DOI: 10.1186/s12977-018-0394-5

[…] in the following order: host rrna; virus rna; host refseq mrna; host non-coding rna. reads which did not align to any of the aforementioned databases were then mapped to the host genome using star [39], again allowing a maximum of 2 mismatches per alignment., to normalize for different library sizes, reads per million mapped reads (rpm) values were calculated using the sum […]

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!