StringTie specifications

Information


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

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StringTie article

StringTie citations

 (6)
2018
PMCID: 5930813

[…] 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 […]

2017
PMCID: 5744951

[…] bowtie2 v.2.2.6 [63, 64]. the abundance of transcript isoforms (tpm–transcripts per million[65]) was determined using stringtie v1.1.2 [66]. expression values were extracted from the appropriate stringtie gtf output files and welch’s unequal variances t-test was performed on transcript level in order to identify differentially expressed transcripts. the resulting set of transcripts […]

2017
PMCID: 5624873

[…] recent updated n. tabacum k326 assembly40 was used as the reference to guide transcript assembly, and this method generated 99,547 transcripts from 66,700 super gene loci by using software hisat and stringtie according to previously described protocols41. the gene number obtained here is close to the estimate number 69,50040. of these gene loci, 37,759 (57%) were identical to existing gene […]

2017
PMCID: 5737200

[…] annotated from modencode project (29, 30) and updated in the current version of drosophila reference genome (release 6) (14), we performed an alternate gene expression analysis workflow provided by stringtie which generates no novel isoforms. we ran the tools using default parameters. the output predicted a total of 66 864 new transcripts in the three mosquito species. in order to reduce false […]

2017
PMCID: 5567338

[…] the correlation coefficients between lncrnas and their potential target genes, and that between the random gene pairs., the quantification of lncrnas and mrnas in each sample was calculated by stringtie. differentially expressed mrnas and lncrnas between low and high sperm motility groups was analyzed using the ballgown (2.6.0) r package54. p-value < 0.05 and |fold-change| > 1.5 […]

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

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