StringTie protocols

StringTie specifications


Unique identifier OMICS_07226
Name StringTie
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License Artistic License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes



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  • person_outline Steven Salzberg <>

Publication for StringTie

StringTie IN pipelines

PMCID: 5827656
PMID: 29507754
DOI: 10.1038/s41421-018-0011-8

[…] of low quality bases is over 50% in read). clean data were aligned to the mouse genome (mm10) using hisat2 with default parameters49. htseq was used to calculate the raw counts for each sample50. stringtie was used to estimate the expression level of the detected genes as fpkm values51. edger was used to evaluate the statistical significance of degs and the additive linear model was utilized […]

PMCID: 5877643
PMID: 29534430
DOI: 10.3390/ijms19030782

[…] and low-quality sequences. mapping of 24 sample reads to wheat genome (t. aestivum. tgacv1) was conducted with tophat (version 2.1.0, default parameters). the new transcripts were assembled with stringtie (version 1.3.3b, default parameters). new gtf assembling and merging for each sample were used known tgac gtf (version: tgacv1)., all of the sequencing data in this study are stored […]

PMCID: 5895686
PMID: 29417162
DOI: 10.1007/s00122-018-3065-y

[…] extseq 500 to obtain single-end 75 bp reads. reads were aligned to the 12x.2 version of the grapevine reference genome pn40024 using hisat2 (kim et al. 2015) and the transcriptome was assembled using stringtie (pertea et al. 2015) with the cribi functional annotation (vitulo et al. 2014). transcribed genes were analyzed by fitting a linear model \documentclass[12pt]{minimal} \usepackage{amsmat […]

PMCID: 5930813
PMID: 29716542
DOI: 10.1186/s12864-018-4654-5

[…] reads were also removed. thereafter, the resulting clean reads were mapped against the p. falciparum genome (plasmodb v26) using hisat2 [48]. the abundance of each reference gene was estimated with stringtie [49]. relative transcriptional activity of each euchromatic gene was assessed using transcripts per million (tpm). when tpm < 1, it was adjusted to be 1. all expression values […]

PMCID: 5515834
PMID: 28769960
DOI: 10.3389/fpls.2017.01257

[…] diagram. genes with a divergence probability (pnoi) ≥ 0.8 and log2 fold-change ≥ 2 were defined as significantly enriched (benjamini and hochberg, 1995). novel transcripts were reconstructed using stringtie (pertea et al., 2015)., the go seq r package was used for gene ontology (go) analysis of degs, and go terms with an adjusted p-value < 0.05 were considered significantly enriched in degs […]

StringTie institution(s)
Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
StringTie funding source(s)
Supported in part by US National Institutes of Health grants R01-HG006677, R01- HG006102, R01-GM105705, R01-CA120185, P01-CA134292, and the Cancer Prevention and Research Institute of Texas.

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