The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes

doi:10.1109/GlobalSIP.2014.7032351

CORC > 北京大学 > 工学院

	The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes
	Yang Cheng ; Wu Po-Yen ; Phan John H ; Wang May D
刊名	... IEEE Global Conference on Signal and Information Processing. IEEE Global Conference on Signal and Information Processing
	2014
DOI	10.1109/GlobalSIP.2014.7032351
英文摘要	RNA-seq data analysis pipelines are generally composed of sequence alignment, expression quantification, expression normalization, and differentially expressed gene (DEG) detection. Each step has numerous specific tools or algorithms, so we cannot explore all combinatorial pipelines and provide a comprehensive comparison of pipeline performance. To understand the mechanism of RNA-seq data analysis pipelines and provide some useful information for pipeline selection, we believe it is necessary to analyze the interactions among pipeline components. In this paper, by combining different alignment algorithms with the same quantification, normalization, and DEG detection tools, we construct nine RNA-seq pipelines to analyze the impact of RNA-seq alignment on downstream applications of gene expression estimates. Specifically, we find moderate linear correlation between the number of DEGs detected and the percentage of reads aligned with zero mismatch.; PubMed; 1376-1379; 2012
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/496558]
专题	工学院
推荐引用方式 GB/T 7714	Yang Cheng,Wu Po-Yen,Phan John H,et al. The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes[J]. ... IEEE Global Conference on Signal and Information Processing. IEEE Global Conference on Signal and Information Processing,2014.
APA	Yang Cheng,Wu Po-Yen,Phan John H,&Wang May D.(2014).The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes.... IEEE Global Conference on Signal and Information Processing. IEEE Global Conference on Signal and Information Processing.
MLA	Yang Cheng,et al."The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes".... IEEE Global Conference on Signal and Information Processing. IEEE Global Conference on Signal and Information Processing (2014).