NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq

Kan Liu, Shangang Jia, Qian Du, Chi Zhang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

After the next-generation sequencing technology, long-read sequencing technologies were developed. Both the advantages and the drawbacks of long-read sequencing technologies are obvious. Here, we take advantages of long-read sequencing technology, MinION, to develop a comprehensive and user-friendly pipeline, NanoAsPipe, to identify the transcriptomic profiles, isoform profiles, and alternative splicing (AS) events of long-read RNA-seq data on the Open Science Grid (OSG). NanoAsPipe includes RNA-seq data preprocessing, mapping and alternative splicing analysis to simultaneously account for AS events. NanoAsPipe was applied to two long-read datasets and its performance was evaluated by comparing discovered AS events with gene annotation and results from short-read RNA-seq data. Majority of predicted AS events by NanoAsPipe was confirmed by the gene annotation and there is a high correlation between results from long-read data and short-read data. NanoAsPipe was implemented as a software package, which is available for academic research at http://sysbio.unl.edu/NanoAsPipe. The user may run the workflow based on the OSG environment or switch it to other computing setup environments.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1823-1826
Number of pages4
ISBN (Electronic)9781509030491
DOIs
StatePublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Publication series

NameProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume2017-January

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Fingerprint

Alternative Splicing
Gene Expression Profiling
RNA
Pipelines
Technology
Molecular Sequence Annotation
Genes
Software packages
Workflow
Switches
Protein Isoforms
Software
Research

Keywords

  • Gene expression
  • MinION
  • Open Science Grid
  • alternative splicing
  • long-read RNA-seq

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Liu, K., Jia, S., Du, Q., & Zhang, C. (2017). NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C-R. Shyu, Y. Bromberg, J. Gao, ... D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 1823-1826). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217937

NanoAsPipe : A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. / Liu, Kan; Jia, Shangang; Du, Qian; Zhang, Chi.

Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1823-1826 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Liu, K, Jia, S, Du, Q & Zhang, C 2017, NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 1823-1826, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217937
Liu K, Jia S, Du Q, Zhang C. NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu C-R, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1823-1826. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). https://doi.org/10.1109/BIBM.2017.8217937
Liu, Kan ; Jia, Shangang ; Du, Qian ; Zhang, Chi. / NanoAsPipe : A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1823-1826 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).
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