共 22 条
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
被引:200
作者:

Au, Kin Fai
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机构:
Stanford Univ, Dept Stat, Stanford, CA 94305 USA Stanford Univ, Dept Stat, Stanford, CA 94305 USA

Jiang, Hui
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机构:
Stanford Univ, Dept Stat, Stanford, CA 94305 USA
Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA Stanford Univ, Dept Stat, Stanford, CA 94305 USA

Lin, Lan
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机构:
Univ Iowa, Dept Internal Med, Iowa City, IA 52242 USA
Univ Iowa, Dept Biomed Engn, Iowa City, IA 52242 USA Stanford Univ, Dept Stat, Stanford, CA 94305 USA

Xing, Yi
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机构:
Univ Iowa, Dept Internal Med, Iowa City, IA 52242 USA
Univ Iowa, Dept Biomed Engn, Iowa City, IA 52242 USA Stanford Univ, Dept Stat, Stanford, CA 94305 USA

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机构:
[1] Stanford Univ, Dept Stat, Stanford, CA 94305 USA
[2] Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA
[3] Univ Iowa, Dept Internal Med, Iowa City, IA 52242 USA
[4] Univ Iowa, Dept Biomed Engn, Iowa City, IA 52242 USA
基金:
美国国家卫生研究院;
关键词:
GENE;
TRANSCRIPTOME;
D O I:
10.1093/nar/gkq211
中图分类号:
Q5 [生物化学];
Q7 [分子生物学];
学科分类号:
071010 ;
081704 ;
摘要:
Alternative splicing is a prevalent post-transcriptional process, which is not only important to normal cellular function but is also involved in human diseases. The newly developed second generation sequencing technique provides high-throughput data (RNA-seq data) to study alternative splicing events in different types of cells. Here, we present a computational method, SpliceMap, to detect splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50-100 nt) and can exploit paired-read information to improve mapping accuracy. Several parameters are included in the output to indicate the reliability of the predicted junction and help filter out false predictions. We applied SpliceMap to analyze 23 million paired 50-nt reads from human brain tissue. The results show at this depth of sequencing, RNA-seq can support reliable detection of splice junctions except for those that are present at very low level. Compared to current methods, SpliceMap can achieve 12% higher sensitivity without sacrificing specificity.
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页码:4570 / 4578
页数:9
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