TopHat-Fusion pipeline

TopHat-Fusion specifications

Information


Unique identifier OMICS_01359
Name TopHat-Fusion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Daehwan Kim <>

Publication for TopHat-Fusion

TopHat-Fusion IN pipelines

 (6)
2018
PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] rna sample preparation v2 guide, illumina company ltd)., htseq software was used to count the reads numbers mapped to each circrna. rpm (reads per million mapped reads, including tophat mapping and tophat-fusion mapping) [1] was employed to calculate the expression level of individual circrna. differential expression between circrnas was assessed by degseq algorithm. we defined the statistical […]

2017
PMCID: 5520850
PMID: 28281539
DOI: 10.1038/cr.2017.31

[…] of corresponding window in control samples., we detected circrna using circexplorer pipeline. first reads were aligned to grch37 human genome with tophat, and then unmapped reads were realigned with tophat-fusion. finally, back-spliced junction reads were annotated with refseq gene annotation., proteins were precipitated with trichloroacetic acid. the protein pellet was dried either by air […]

2016
PMCID: 4868023
PMID: 27179618
DOI: 10.1186/s13023-016-0439-6

[…] a gene-fusion between exon 1 of plekhg3 (chr14: 65,171,193-65,171,422) and exon 4 of tcf4 (nm_001083962.1; chr18: 53,131,307-53,131,368); 4 paired-end reads and 11 single reads spanned the junction (tophat fusion and blat alignment of unaligned reads) (data not shown). this analysis did not detect a fusion transcript between tcf4 and dynap. rt-pcr of skin fibroblast total rna and sanger […]

2015
PMCID: 4380965
PMID: 25594743
DOI: 10.1002/cam4.360

[…] variants are called. this approach for calling variants from rna-seq has been validated previously 30. the pipeline uses the popular tophat-cufflinks protocol 31 produce gene expression results and tophat-fusion 32 to detect potential fusions., this pipeline analyzes variants from the exome or transcriptome pipeline to identify rare, deleterious (rd) variants and also druggable rd variants […]

2015
PMCID: 4656206
PMID: 26349458
DOI: 10.1007/s13238-015-0202-0

[…] the continuous decrease of sequencing cost, rna-seq become the most prevalent method for identification of circrnas. although a few bioinformatic algorithms such as mapsplice (wang et al., 2010), tophat-fusion (kim and salzberg, 2011), and ciri (gao et al., 2015) were developed for global discovery of circular rnas, the consistency of these computational tools remains relatively low. rnase r […]

TopHat-Fusion institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
TopHat-Fusion funding source(s)
Supported in part by NIH grants R01- LM006845 and R01-HG006102.

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