Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
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Snaptron：查询数万个 RNA-seq 样本的剪接模式。
DOI：
10.1093/bioinformatics/btx547
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发表时间：
2018
期刊：
影响因子：
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通讯作者：
Langmead,Ben
中科院分区：
文献类型：
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作者：
Wilks,Christopher;Gaddipati,Phani;Nellore,Abhinav;Langmead,Ben
动机随着越来越多、规模更大的基因组学研究的出现，对全面且可查询的交叉研究总结的需求日益增长。这些使研究人员能够利用难以获得的大量数据集。ResultsSnaptron 是一个汇总 RNA 测序数据的搜索引擎，带有查询规划器，利用 R 树、B 树和倒排索引策略快速执行来自 70 多个人类 RNA-seq 样本的超过 1.46 亿个外显子-外显子剪接点的查询。可以通过限制要考虑的连接点和样本来定制查询。 Snaptron可以根据组织特异性或其他标准对连接点进行评分，并且可以根据不同剪接模式的相对频率对样本进行评分。我们描述了该软件并概述了可以通过 Snaptron 查询探索的生物学问题。可用性和实施文档位于 http://snaptron.cs.jhu.edu。源代码位于 https://github.com/ChristopherWilks/snaptron 和 https://github.com/ChristopherWilks/snaptron-experiments，具有 CC BY-NC 4.0 许可证。补充信息补充数据可在生物信息学在线获取。
MotivationAs more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain.ResultsSnaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70 000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can score junctions according to tissue specificity or other criteria, and can score samples according to the relative frequency of different splicing patterns. We describe the software and outline biological questions that can be explored with Snaptron queries.Availability and implementationDocumentation is at http://snaptron.cs.jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron and https://github.com/ChristopherWilks/snaptron-experiments with a CC BY-NC 4.0 license.Supplementary informationSupplementary data are available atBioinformaticsonline.