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
Publication statusPublished - 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

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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