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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




No version available


  • person_outline Steven Salzberg

Publication for StringTie

StringTie citations


Basic leucine zipper transcription factor SlbZIP1 mediates salt and drought stress tolerance in tomato

BMC Plant Biol
PMCID: 5941487
PMID: 29739325
DOI: 10.1186/s12870-018-1299-0
call_split See protocol

[…] y mapped to the tomato reference genome by HISAT2 software []. The quantitative information of the RNA-seq data can be seen in Additional file : Table S3. Gene expression abundance was analyzed using StringTie software [], to identify DEGs (differentially expressed genes), transcript abundance was normalized by FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions bas […]


In depth comparative analysis of malaria parasite genomes reveals protein coding genes linked to human disease in Plasmodium falciparum genome

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

[…] ted reads were also removed. Thereafter, the resulting clean reads were mapped against the P. falciparum genome (PlasmoDB v26) using HISAT2 []. The abundance of each reference gene was estimated with StringTie []. 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 were log2-scaled […]


Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential

BMC Genomics
PMCID: 5930858
PMID: 29716547
DOI: 10.1186/s12864-018-4723-9
call_split See protocol

[…] med from the 3′ end of reads with Cutadapt []. Hisat2 [] was used to map reads to the reference genome Galgal5.0 ( Duplicate reads were then removed. Stringtie [] was used to define the transcripts from the read mappings for each sample, and to merge the transcript definitions for all samples. Transcripts were cleaned up using in-house scripts. The […]


Position specific intron retention is mediated by the histone methyltransferase SDG725

BMC Biol
PMCID: 5925840
PMID: 29706137
DOI: 10.1186/s12915-018-0513-8
call_split See protocol

[…] xtraction, followed by RNA-seq library preparation and sequencing as described above. After quality control, the raw sequenced reads were aligned to the rice reference genome as described above, then StringTie was used to assemble transcripts for each sample and combine them together with Cuffcompare, a subpackage of Cufflinks []. Then the annotated unique start codon located on the assembled tran […]


Widespread intronic polyadenylation diversifies immune cell transcriptomes

Nat Commun
PMCID: 5928244
PMID: 29712909
DOI: 10.1038/s41467-018-04112-z

[…] The complete transcript structure was obtained through the following steps. (i) We used StringTie, an improved method for more accurate de novo assembly of transcripts from RNA-seq data. De novo assembly was performed on every RNA-seq sample with default settings using the hg19 RefSeq an […]


Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] r downstream, and on the same or opposite strand (if < 5 kb from the nearest TSS), or (c) intergenic (if ≥ 5, 10, 20, 50, 100, 500 kb or 1 Mb from the nearest TSS, irrespective of strand). The HISAT2/StringTie pipeline, used to generate these transcript models, could not infer the transcription strand in all cases, particularly for single-exon transcripts. Accordingly, some lncRNAs will overlap th […]

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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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