Introduction

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.

Publications

  1. SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.
    Cite this
    Davidson NM, Hawkins ADK, Oshlack A, 2017-08-01 - Genome biology

Credits

  1. Nadia M Davidson
    Developer

    School of BioSciences, University of Melbourne

  2. Anthony D K Hawkins
    Developer

    Murdoch Children's Research Institute, Royal Children's Hospital, Australia

  3. Alicia Oshlack
    Investigator

    School of BioSciences, University of Melbourne

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Summary
AccessionBT000143
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByAlicia Oshlack