@inproceedings{00710cb38fae4ecb8733d621279c852b,
title = "NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq",
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.",
keywords = "Gene expression, MinION, Open Science Grid, alternative splicing, long-read RNA-seq",
author = "Kan Liu and Shangang Jia and Qian Du and Chi Zhang",
note = "Funding Information: ACKNOWLEDGMENT The authors thank Weilong Yang and Dr. Huihui Yu for their assistance in the sequence processing. Thanks to Dr. Qi Zhang for his advice on the statistical support of the data analysis. All authors edited the manuscript. There are no competing financial interests of this research. This study was supported in part by Nebraska Soybean Board funds. Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",
year = "2017",
month = dec,
day = "15",
doi = "10.1109/BIBM.2017.8217937",
language = "English (US)",
series = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "1823--1826",
editor = "Illhoi Yoo and Zheng, {Jane Huiru} and Yang Gong and Hu, {Xiaohua Tony} and Chi-Ren Shyu and Yana Bromberg and Jean Gao and Dmitry Korkin",
booktitle = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",
}