TopHat-Fusion protocols

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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

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Maintainer


  • person_outline Daehwan Kim <>

Publication for TopHat-Fusion

TopHat-Fusion in pipelines

 (10)
2018
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] sam was further processed with the picard tool to recalibrate reads. finally, we called and filtered variants using the haplotype caller from gatk. fusion transcripts were obtained with the tophat-fusion pipeline. to quantify differentially-expressed transcripts, we realigned and processed., rnaseq data from 10 normal human fibroblasts samples (geo dataset gse51518 from the ncbi) […]

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) [] 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: 5430301
PMID: 28555173
DOI: 10.3389/fonc.2017.00094

[…] the two models treated to acquired resistance (cu_tnbc_002 and cu_tnbc_005), we did not identify any new mutations at the time of acquired resistance. similarly, we performed fusion detections using tophat-fusion on these acquired resistance models and did not identify any new fusions at the time of acquired resistance., treatment with enmd-2076 200 mg/kg daily with continuous dosing resulted […]

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 […]

2017
PMCID: 5702394
PMID: 29259349
DOI: 10.1155/2017/6870614

[…] applying tophat alignment v1.0. tophat alignment workflow allows the following functions: (i) read mapping on homo sapiens ucsc hg19 through the tophat 2 aligner and (ii) fusion calling with tophat-fusion []. after the alignment of sequencing reads within the exon regions, the reads not entirely aligned were divided into multiple segments of 25 bp. it is expected that the initially […]


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TopHat-Fusion in publications

 (61)
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] significantly downregulated genes associated with vasculogenesis compared to the other ggns (fig. ).figure 2figure 3figure 4, a total of five fusion gene loci were detected in four ggns using the tophat fusion tool as follows (table  and supplementary fig. ): mediator complex subunit 13-like (med13l) → tudor domain containing 3 (tdrd3) in ggn3, sterile alpha motif domain containing 12 […]

PMCID: 5927466
PMID: 29668680
DOI: 10.1371/journal.pbio.2005707

[…] 126-nt paired-end reads per individual sample (7–8 flow cell lanes/sample), which were aligned to the hg19 human reference genome (genome reference consortium grch37 from february 2009) [] with tophat-fusion function []. composite rpkm counts within genomic coordinates of 20,304 nonhaplotype hgnc-annotated genes were used to calculate gene expression differences based on log2-transformed […]

PMCID: 5961503
PMID: 29617664
DOI: 10.1016/j.celrep.2018.03.076

[…] involving 224 ddr genes. among these, 464 fgs including 173 ddr genes were derived from tcga cancer samples. to reduce false positives, we used read count information together with fusionscan, tophat-fusion, and prada. following their filtering criteria, we used fusion transcripts having ≥ 2 seed/junction reads for fusionscan and prada analyses, and those with ≥ 100 spanning pairs […]

PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] in a gene set are harmoniously up- or down-regulated in a sample., to reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. we first applied four tools—tophat-fusion (), mapsplice (), fusionmap (), and prada ()—to detect putative fusions in our nine pairs of frozen wd/dd samples. then, fusions with at least one junction read and at least two […]

PMCID: 5845222
PMID: 29523209
DOI: 10.1186/s13287-018-0793-5

[…] sequence reads were first multiply mapped against the grch37/hg19 human reference genome using tophat 2.1. unmapped reads were then extracted and mapped onto the relevant reference genome using tophat-fusion. reads that split and aligned on the same chromosome but in noncollinear ordering were extracted as candidate back-spliced junction reads. back-spliced junction reads […]


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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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