Introduction

Analysis of RNA-seq data often detects numerous 'non-co-linear' (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method ('NCLscan'), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.

Publications

  1. NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.
    Cite this
    Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY, 2016-02-01 - Nucleic acids research

Credits

  1. Trees-Juen Chuang
    Developer

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

  2. Chan-Shuo Wu
    Developer

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

  3. Chia-Ying Chen
    Developer

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

  4. Li-Yuan Hung
    Developer

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

  5. Tai-Wei Chiang
    Developer

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

  6. Min-Yu Yang
    Investigator

    Division of Physical and Computational Genomics, Genomics Research Center, Taiwan, Province of China

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Summary
AccessionBT006909
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionTaiwan, Province of China
Submitted ByMin-Yu Yang