title: NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.
abstract: 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.
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan trees@gate.sinica.edu.tw.
authors.forename: Trees-Juen
authors.initials: TJ
authors.lastname: Chuang
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Chan-Shuo
authors.initials: CS
authors.lastname: Wu
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Chia-Ying
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Li-Yuan
authors.initials: LY
authors.lastname: Hung
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Tai-Wei
authors.initials: TW
authors.lastname: Chiang
authors.affiliation: Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Min-Yu
authors.initials: MY
authors.lastname: Yang
mesh_terms: D057230:Limit of Detection; D012313:RNA / Q000235:genetics*; D012326:RNA Splicing; D000079962:RNA, Circular; D012333:RNA, Messenger / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D000079962:RNA, Circular; D012333:RNA, Messenger; D012313:RNA