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	Hsa: a heuristic splice alignment tool
	Bu,Jingde1,2; Chi,Xuebin1; Jin,Zhong1
刊名	Bmc systems biology
	2013-12-17
卷号	7期号:Suppl 2
ISSN号	1752-0509
DOI	10.1186/1752-0509-7-s2-s10
通讯作者	Jin,zhong(zjin@sccas.cn)
英文摘要	Abstractbackgroundrna-seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of next generation sequencing (ngs). with the high throughput sequencing of rna-seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. but the short read length brings a great challenge to alignment, especially when the reads span two or more exons.methodsa two steps heuristic splice alignment tool is generated in this investigation. first, map raw reads to reference with unspliced aligner - bwa; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match.resultscompare with other splice alignment tools like soapsplice and tophat2, hsa has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent.conclusionshsa is an effective spliced aligner of rna-seq reads mapping, which is available at https://github.com/vlcc/hsa.
语种	英语
出版者	BioMed Central
WOS记录号	BMC:10.1186/1752-0509-7-S2-S10
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2374156
专题	计算机网络信息中心
通讯作者	Jin,Zhong
作者单位	1.Chinese Academy of Sciences; Supercomputing Center, Computer Network Information Center 2.Graduate University of Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Bu,Jingde,Chi,Xuebin,Jin,Zhong. Hsa: a heuristic splice alignment tool[J]. Bmc systems biology,2013,7(Suppl 2).
APA	Bu,Jingde,Chi,Xuebin,&Jin,Zhong.(2013).Hsa: a heuristic splice alignment tool.Bmc systems biology,7(Suppl 2).
MLA	Bu,Jingde,et al."Hsa: a heuristic splice alignment tool".Bmc systems biology 7.Suppl 2(2013).

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