IsoRef improves the reference-based transcriptome assembly accuracy for RNA-seq data

Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45)32_Refereed conference paper (with ISBN/ISSN)peer-review

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Author(s)

Related Research Unit(s)

Detail(s)

Original languageEnglish
Title of host publicationProceedings - 10th International Conference on Bioinformatics and Computational Biology (BICOB 2018)
EditorsHisham Al-Mubaid, Qin Ding, Oliver Eulenstein
PublisherThe International Society for Computers and Their Applications (ISCA)
Pages148-153
ISBN (Print)978-1-5108-5866-4
Publication statusPublished - Mar 2018

Conference

Title10th International Conference on Bioinformatics and Computational Biology, BICOB 2018
PlaceUnited States
CityLas Vegas
Period19 - 21 March 2018

Abstract

Transcript reconstruction from mammal RNA-Seq data remains a challenging problem due to several biases, such as those from sequencing or mapping, the complexity of mammalian transcriptome generation from alternative splicing, fragmentary characteristics of reads, and from the unbalanced sequencing. Here, IsoRef, a reference-based transcriptome assembler for RNA-Seq data, is proposed. IsoRef investigates information from not only sequencing data, but from transcript annotation as well, in order to build accurate splice graphs. A ?ow balancing technique is proposed to reduce the impact of false positive transcripts and to narrow the search space of true positive transcripts. For each of two in silico datasets, IsoRef predicted 1,400 additional correct transcripts than StringTie; for each of the fve actual datasets, IsoRef identifed at least 1,500 additional correct transcripts than StringTie, which improves the transcript-level and gene-level accuracy compared to StringTie with a maximum improvement of 20%. IsoRef is available at deepomics.org/module-instances/2CA682222F734424/.

Research Area(s)

  • Flowbalance graph, Splice graph, Transcriptome assembly

Bibliographic Note

“Full text of this publication does not contain sufficient affiliation information. With consent from the author(s) concerned, the Research Unit(s) information for this record is based on the existing academic department affiliation of the author(s).

Citation Format(s)

IsoRef improves the reference-based transcriptome assembly accuracy for RNA-seq data. / Ao, Xiang; Zhao, Zicheng; Li, Shuaicheng.

Proceedings - 10th International Conference on Bioinformatics and Computational Biology (BICOB 2018). ed. / Hisham Al-Mubaid; Qin Ding; Oliver Eulenstein. The International Society for Computers and Their Applications (ISCA), 2018. p. 148-153.

Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45)32_Refereed conference paper (with ISBN/ISSN)peer-review