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    SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

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    Author
    Davidson, NM; Hawkins, ADK; Oshlack, A
    Date
    2017-08-04
    Source Title
    Genome Biology
    Publisher
    BIOMED CENTRAL LTD
    University of Melbourne Author/s
    Davidson, Nadia; Oshlack, Alicia
    Affiliation
    School of BioSciences
    School of Physics
    Metadata
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    Document Type
    Journal Article
    Citations
    Davidson, N. M., Hawkins, A. D. K. & Oshlack, A. (2017). SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. GENOME BIOLOGY, 18 (1), https://doi.org/10.1186/s13059-017-1284-1.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256880
    DOI
    10.1186/s13059-017-1284-1
    Abstract
    Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms. We further use Lace to combine reference and assembled transcriptomes for chicken and recover hundreds of gaps in the reference genome.

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