NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq
作者： Kan Liu , Shangang Jia , Qian Du , Chi Zhang
DOI: 10.1109/BIBM.2017.8217937
关键词:
摘要: After the next-generation sequencing technology, long-read technologies were developed. Both advantages and drawbacks of are obvious. Here, we take MinION, to develop a comprehensive user-friendly pipeline, NanoAsPipe, identify transcriptomic profiles, isoform alternative splicing (AS) events RNA-seq data on Open Science Grid (OSG). NanoAsPipe includes preprocessing, mapping analysis simultaneously account for AS events. was applied two datasets its performance evaluated by comparing discovered with gene annotation results from short-read data. Majority predicted confirmed there is high correlation between implemented as software package, which available academic research at http://sysbio.unl.edu/NanoAsPipe. The user may run workflow based OSG environment or switch it other computing setup environments.
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sci-hub.se 参考文章(23)
Weichen Wang, Zhiyi Qin, Zhixing Feng, Xi Wang, Xuegong Zhang, Identifying differentially spliced genes from two groups of RNA-seq samples. Gene. ,vol. 518, pp. 164- 170 ,(2013) , 10.1016/J.GENE.2012.11.045
Gene W Yeo, Eric Van Nostrand, Dirk Holste, Tomaso Poggio, Christopher B Burge, Identification and analysis of alternative splicing events conserved in human and mouse. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 2850- 2855 ,(2005) , 10.1073/PNAS.0409742102
Miten Jain, Ian T Fiddes, Karen H Miga, Hugh E Olsen, Benedict Paten, Mark Akeson, Improved data analysis for the MinION nanopore sequencer Nature Methods. ,vol. 12, pp. 351- 356 ,(2015) , 10.1038/NMETH.3290
Ruolin Liu, Ann E Loraine, Julie A Dickerson, Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems BMC Bioinformatics. ,vol. 15, pp. 364- 364 ,(2014) , 10.1186/S12859-014-0364-4
Shihao Shen, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D. Henry, Ying Nian Wu, Qing Zhou, Yi Xing, rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, ,(2014) , 10.1073/PNAS.1419161111
Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics. ,vol. 26, pp. 841- 842 ,(2010) , 10.1093/BIOINFORMATICS/BTQ033
Alex K. Shalek, Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury, Schraga Schwartz, Nir Yosef, Christine Malboeuf, Diana Lu, John J. Trombetta, Dave Gennert, Andreas Gnirke, Alon Goren, Nir Hacohen, Joshua Z. Levin, Hongkun Park, Aviv Regev, Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Nature. ,vol. 498, pp. 236- 240 ,(2013) , 10.1038/NATURE12172
Anthony M. Bolger, Marc Lohse, Bjoern Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data Bioinformatics. ,vol. 30, pp. 2114- 2120 ,(2014) , 10.1093/BIOINFORMATICS/BTU170
Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang, SpliceTrap: a method to quantify alternative splicing under single cellular conditions Bioinformatics. ,vol. 27, pp. 3010- 3016 ,(2011) , 10.1093/BIOINFORMATICS/BTR508
A.E. Loraine, G.A. Helt, M.S. Cline, M.A. Siani-Rose, Protein-based analysis of alternative splicing in the human genome computational systems bioinformatics. ,vol. 1, pp. 118- 124 ,(2002) , 10.1109/CSB.2002.1039335