We are analyzing https://link.springer.com/article/10.1186/gb-2011-12-8-r72.

Title:
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts | Genome Biology
Description:
TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/ .
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Keywords {🔍}

fusion, reads, tophatfusion, fusions, read, pubmed, data, genes, article, figure, gene, cell, reported, file, chromosome, rnaseq, google, scholar, cancer, genome, alignment, pairedend, additional, pairs, point, segment, cas, transcripts, central, table, segments, alignments, mate, number, candidates, found, full, breast, map, false, spanning, supporting, multiple, bowtie, mapping, fusionseq, mcf, line, mapped, original,

Topics {✒️}

keywords=e-mtab-513&expandefo= inter-transcript paired-end reads paired-end rna-seq reads paired-end rna-sequencing related subjects nih grants r01-lm006845 full size image article number r72 article download pdf single-base precision enabled paired-end transcriptome sequencing bcr/abl1 gene fusion bcr-abl1 fusion gene rna-seq data sets aligns rna-seq reads assemble rna-seq reads analyze rna-seq experiments tumor rna-seq data fusion genes homez-myh6 cancer cell lines uhr paired-end reads intra-chromosomal fusion product vcap paired-end reads multiple cell lines rna-seq data set full-length read alignment paired-end reads mapped tophat-fusion website [21] uhr single-end reads open source software differential gene expression mcf7 cell line tophat-fusion outputs alignments breast cancer data sequence alignment/map format full access mcf7 cell lines tophat-fusion prefers reads privacy choices/manage cookies finds events involving download web page base-pair resolution broadway research building discover genes created fusions tophat-fusion missed open-source bowtie finding candidate fusions lder = square root rna sequence analysis paired-end data

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Schema {🗺️}

WebPage:
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         headline:TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
         description:TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/ .
         datePublished:2011-08-11T00:00:00Z
         dateModified:2011-08-11T00:00:00Z
         pageStart:1
         pageEnd:15
         license:http://creativecommons.org/licenses/by/2.0/
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            Fusion Gene
            Fusion Transcript
            Fusion Event
            Mate Pair
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
      description:TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/ .
      datePublished:2011-08-11T00:00:00Z
      dateModified:2011-08-11T00:00:00Z
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         Fusion Gene
         Fusion Transcript
         Fusion Event
         Mate Pair
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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               type:PostalAddress
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      email:[email protected]
      name:Steven L Salzberg
      affiliation:
            name:University of Maryland
            address:
               name:Center for Bioinformatics and Computational Biology, 3115 Biomolecular Sciences Building #296, University of Maryland, College Park, USA
               type:PostalAddress
            type:Organization
            name:Johns Hopkins University School of Medicine
            address:
               name:McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
               type:PostalAddress
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            address:
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      name:Center for Bioinformatics and Computational Biology, 3115 Biomolecular Sciences Building #296, University of Maryland, College Park, USA
      name:McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
      name:Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, USA

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