Metrics for rapid quality control in RNA structure probing experiments
Metrics for rapid quality control in RNA structure probing experiments
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DOI：
10.1093/bioinformatics/btw501
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发表时间：
2016-12-01
期刊：
影响因子：
5.8
通讯作者：
Aviran, Sharon
中科院分区：
文献类型：
--
作者：
Choudhary, Krishna;Shih, Nathan P.;Aviran, Sharon
动机：RNA的不同功能可以归因于其形成复杂和多样结构的能力。最近，新的结构探测技术与高通量测序相结合，帮助RNA研究在范围和深度上都有所扩展。尽管技术上存在差异，但由于化学探测和测序的随机性，大多数实验在再现性方面面临类似的挑战。随着这些方案扩展到转录组范围的研究，质量控制成为一项更加艰巨的任务。一般和有效的方法是需要量化的变异性和质量在广泛的当前和新兴的结构探测experiments.Results：我们开发的指标，以快速和定量评估数据质量的结构探测实验，证明他们的效率小的合成库和转录组范围内的数据集。我们使用信噪比的概念来评估重复协议，它有能力识别高质量的数据。我们还考虑和比较两种方法来评估探测实验中固有的变异性，然后利用它来评估满足所需质量所需的覆盖范围调整。开发的指标和工具将有助于总结大规模数据集，并将有助于标准化该领域的质量控制。
Motivation: The diverse functionalities of RNA can be attributed to its capacity to form complex and varied structures. The recent proliferation of new structure probing techniques coupled with high-throughput sequencing has helped RNA studies expand in both scope and depth. Despite differences in techniques, most experiments face similar challenges in reproducibility due to the stochastic nature of chemical probing and sequencing. As these protocols expand to transcriptome-wide studies, quality control becomes a more daunting task. General and efficient methodologies are needed to quantify variability and quality in the wide range of current and emerging structure probing experiments.Results: We develop metrics to rapidly and quantitatively evaluate data quality from structure probing experiments, demonstrating their efficacy on both small synthetic libraries and transcriptome-wide datasets. We use a signal-to-noise ratio concept to evaluate replicate agreement, which has the capacity to identify high-quality data. We also consider and compare two methods to assess variability inherent in probing experiments, which we then utilize to evaluate the coverage adjustments needed to meet desired quality. The developed metrics and tools will be useful in summarizing large-scale datasets and will help standardize quality control in the field.