StringTie protocols

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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
Programming languages C++
License Artistic License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Steven Salzberg <>

Publication for StringTie

StringTie in pipelines

 (26)
2018
PMCID: 5820551
PMID: 29568765
DOI: 10.1155/2018/8134902

[…] the clean reads were mapped to the mice reference genome based on ncbi by tophat software. the gene expression values using fragments per kilobase of exon model per million reads were obtained by stringtie tool (v1.2.2) based on mice gene annotation., degs between cells with aβ1–42 samples and cells with aβ1–42 + cur samples were obtained using the linear model for microarray package in r []. […]

2018
PMCID: 5864929
PMID: 29615930
DOI: 10.3389/fphys.2018.00236

[…] and sequenced on an illumina hiseq 2000 sequencer, following the manufacturer's instructions. after filtered, the clean reads were aligned to human genome hg19 based on hisat and assembled by stringtie (li et al., ). the expression value of each transcript was subsequently calculated based on methods of fragments per kilobase of exon model per million mapped fragments (fpkm). in addition, […]

2018
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 […]

2018
PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] sheep lncrnas (14,862 of which are multi-exonic) and 7671 candidate goat lncrnas (3289 of which are multi-exonic). the sheep genome, oar v3.1, already contains 1858 lncrna models, of which the stringtie assembly precisely reconstructs 1402 (75%). in spite of this pre-existing support, these models were included on the sheep longlist for independent verification. the goat genome, […]

2017
PMCID: 5321795
PMID: 28221375
DOI: 10.1038/ncomms14529

[…] similar to several llcs (). this suggests that clk-independent mechanisms also contribute to rhythmic upregulation of per and some llcs during os., we performed de novo transcript assembly using stringtie and cuffmerge and found 154 unannotated genes with multi-exonic transcripts (). twenty two of these were rhythmic in old flies (), and five exhibited llc-like behaviour (). among […]


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StringTie in publications

 (122)
PMCID: 5941487
PMID: 29739325
DOI: 10.1186/s12870-018-1299-0

[…] 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 […]

PMCID: 5930858
PMID: 29716547
DOI: 10.1186/s12864-018-4723-9

[…] from the 3′ end of reads with cutadapt []. hisat2 [] was used to map reads to the reference genome galgal5.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/gallus_gallus). 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. […]

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 []. 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 […]

PMCID: 5925840
PMID: 29706137
DOI: 10.1186/s12915-018-0513-8

[…] 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 […]

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

[…] the first tmd was determined as: (upstream cdr from ipa−upstream cdr from the intron before the first tmd)/3., 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 […]


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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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