Introduction

High throughput RNA sequencing (RNA-Seq) can generate whole transcriptome information at the single transcript level providing a powerful tool with multiple interrelated applications including transcriptome reconstruction and quantification. The sequences of novel transcripts can be reconstructed from deep RNA-Seq data, but this is computationally challenging due to sequencing errors, uneven coverage of expressed transcripts, and the need to distinguish between highly similar transcripts produced by alternative splicing. Another challenge in transcriptomic analysis comes from the ambiguities in mapping reads to transcripts.We present MaLTA, a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data. Our approach explores transcriptome structure and incorporates a maximum likelihood model into the assembly and quantification procedure. A new version of the IsoEM algorithm suitable for Ion Torrent RNA-Seq reads is used to accurately estimate transcript expression levels. The MaLTA-IsoEM tool is publicly available at: http://alan.cs.gsu.edu/NGS/?q=maltaExperimental results on both synthetic and real datasets show that Ion Torrent RNA-Seq data can be successfully used for transcriptome analyses. Experimental results suggest increased transcriptome assembly and quantification accuracy of MaLTA-IsoEM solution compared to existing state-of-the-art approaches.

Publications

  1. Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
    Cite this
    Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A, 2014-01-01 - BMC genomics

Credits

  1. Serghei Mangul
    Developer

  2. Adrian Caciula
    Developer

  3. Sahar Al Seesi
    Developer

  4. Dumitru Brinza
    Developer

  5. Ion Mӑndoiu
    Developer

  6. Alex Zelikovsky
    Investigator

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Summary
AccessionBT000043
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByAlex Zelikovsky