Observations on novel splice junctions from RNA sequencing data

被引：17

作者：

Wang, Likun ^{[1
,2
]}

Wang, Xiaowo ^{[2
]}

Wang, Xi ^{[2
]}

Liang, Yanchun ^{[1
]}

Zhang, Xuegong ^{[2
]}

机构：

[1] Jilin Univ, Coll Comp Sci & Technol, Changchun 130012, Peoples R China

[2] Tsinghua Univ, MOE Key Lab, Bioinformat & Bioinformat Div, TNLIST Dept Automat, Beijing 100084, Peoples R China

来源：

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS | 2011年 / 409卷 / 02期

基金：

中国国家自然科学基金;

关键词：

RNA sequencing; Alternative splicing; Splice junction detection; Sequencing depth; Differential expression; SINGLE; TRANSCRIPTOME; GENOME;

D O I：

10.1016/j.bbrc.2011.05.005

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：

High-throughput RNA sequencing (RNA-seq) technology provides a revolutionary approach to studying splicing events de nova. However, identifying splice junctions with high sensitivity and specificity remains a challenge. In the present study, we proposed a new tool named SeqSaw to detect splice junctions with or without the canonical GT-AG splicing signal. SeqSaw was applied to two ENCODE RNA-seq datasets and also compared with two existing methods. It was shown that the proposed method obtained better results on finding novel splice junctions. Experiments also revealed that the current sequencing depth has not yet reached saturation to detect novel transcripts. Moreover, by comparing the number of supporting reads, we demonstrated that many un-annotated splicing events can be tissue specific. (C) 2011 Elsevier Inc. All rights reserved.

引用

页码：299 / 303

页数：5

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