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Protocols

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


No version available

Maintainer


  • person_outline Daehwan Kim

Publication for TopHat-Fusion

TopHat-Fusion citations

 (79)
library_books

Genomic alterations of ground glass nodular lung adenocarcinoma

2018
Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] erformed by principal component analysis and hierarchical clustering. Gene ontology analyses were performed by DAVID (https://david.ncifcrf.gov/) and visualized by REVIGO (http://revigo.irb.hr/). The TopHat-fusion tool was used for the detection of fusion gene loci. […]

call_split

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] RNA sequences were aligned to hg19 and organized into de-novo spliced alignments using bowtie2 and TopHat version 2.1.0 (ccb.jhu.edu/software/tophat). Fusion transcripts were detected using chimerascan version 0.4.5a filtered to remove common false positives. RNASeq raw count files were used to construct an expression matrix using Roche's i […]

library_books

RNA Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas

2018
Mol Cancer
PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] eqR 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 cr […]

library_books

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

2018
PLoS Biol
PMCID: 5927466
PMID: 29668680
DOI: 10.1371/journal.pbio.2005707

[…] llion 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 fol […]

library_books

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

2018
Cell Rep
PMCID: 5961503
PMID: 29617664
DOI: 10.1016/j.celrep.2018.03.076

[…] usions 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 for TopHa […]

library_books

Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

2018
PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] 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 supporti […]

Citations

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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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