Computational analysis of bacterial RNA-Seq data.
Computational analysis of bacterial RNA-Seq data.
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DOI：
10.1093/nar/gkt444
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发表时间：
2013-08
影响因子：
14.9
通讯作者：
Tjaden B
中科院分区：
文献类型：
--
作者：
McClure R;Balasubramanian D;Sun Y;Bobrovskyy M;Sumby P;Genco CA;Vanderpool CK;Tjaden B
高通量RNA测序（RNA-seq）的最新进展使我们对细菌转录组的理解取得了巨大的飞跃。然而，用于分析细菌转录组数据的计算方法没有跟上RNA-seq技术产生的大型且不断增长的数据集的步伐。在这里，我们提出了新的算法，特定于细菌基因结构和转录组，用于分析RNA-seq数据。这些算法在一个名为Rockhopper的开源软件系统中实现，该系统支持细菌RNA-seq数据分析的各个阶段，包括将测序读数与基因组对齐，构建转录组图谱，量化转录本丰度，测试差异基因表达，确定操纵子结构和可视化结果。我们使用来自75个RNA-seq实验的21亿个测序读数来证明跳岩企鹅的性能，这些实验使用大肠杆菌、淋病奈瑟菌、肠道沙门氏菌、化脓性链球菌和嗜热棒状杆菌进行。我们发现，我们的算法生成的转录组图谱是高度准确的相比，集中的实验数据从E。coli和N.淋病，我们验证了我们的系统的能力，以确定新的小RNA，操纵子和转录起始位点。我们的研究结果表明，跳岩企鹅可用于细菌RNA-seq数据的有效和准确的分析，它可以帮助阐明细菌转录组。
Recent advances in high-throughput RNA sequencing (RNA-seq) have enabled tremendous leaps forward in our understanding of bacterial transcriptomes. However, computational methods for analysis of bacterial transcriptome data have not kept pace with the large and growing data sets generated by RNA-seq technology. Here, we present new algorithms, specific to bacterial gene structures and transcriptomes, for analysis of RNA-seq data. The algorithms are implemented in an open source software system called Rockhopper that supports various stages of bacterial RNA-seq data analysis, including aligning sequencing reads to a genome, constructing transcriptome maps, quantifying transcript abundance, testing for differential gene expression, determining operon structures and visualizing results. We demonstrate the performance of Rockhopper using 2.1 billion sequenced reads from 75 RNA-seq experiments conducted with Escherichia coli, Neisseria gonorrhoeae, Salmonella enterica, Streptococcus pyogenes and Xenorhabdus nematophila. We find that the transcriptome maps generated by our algorithms are highly accurate when compared with focused experimental data from E. coli and N. gonorrhoeae, and we validate our system’s ability to identify novel small RNAs, operons and transcription start sites. Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
14.9
作者：
Gardner PP;Daub J;Tate J;Moore BL;Osuch IH;Griffiths-Jones S;Finn RD;Nawrocki EP;Kolbe DL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
5.4
作者：
Croucher, Nicholas J.;Thomson, Nicholas R.
通讯作者：
Thomson, Nicholas R.