Beyond heuristics: a tool for the rigorous statistical analysis of *-seq assays.

描述（由申请人提供）：基于下一代测序技术的检测（*-seq检测）在基因组学领域得到广泛应用。随着这些分析方法的成熟，并试图探索更微妙的生物现象，将需要基于强大的统计技术的新工具来为所得到的生物学结论提供信心。迄今为止，*-seq测定分析工具可分为两种不同的类别，制图和定量。绘图工具试图将每个读段与基因组位置相匹配，而量化工具则从“绘制的”读段推断生物学特征。映射的结果通常非常依赖于调优参数，并且很少（如果有的话）提供任何置信度的概念。分析工具通常将所提供的映射视为真理。这个项目将采取不同的方法。研究人员建议使用已知的物理和生化性质的分析来模拟分析。这样的方法将产生更好的映射，同时提供一个信心的概念，可以作为下游分析的一个组成部分。软件和基础模型的广泛验证计划在三个生物体中使用来自五个不同验证实验的数据。本项目提出的工作将显著改善*-seq数据的分析。如果成功，该项目将取代大量的映射算法、峰值调用器和转录量化器，形成一个软件套件的基础，用于*-seq分析的综合分析。

DESCRIPTION (provided by applicant): Assays based upon next generation sequencing technologies (*-seq assays) are widely used in the genomics community. As these assays mature and attempt to probe more subtle biological phenomenon, new tools based upon powerful statistical techniques will be needed to provide confidence in the resulting biological conclusions. To date, *-seq assay analysis tools can be split into two distinct classes, mapping and quantification. Mapping tools attempt to match each read with a genomic location, whereas quantification tools infer biological features from the "mapped" reads. The results of the mapping are often very dependent on tuning parameters and rarely, if ever, provide any notion of confidence. The analysis tools typically take the provided mappings as gospel. This project will take a different approach. The investigators propose to use known physical and biochemical properties of the assay to model the assay. Such an approach will yield better mappings, while providing a notion of confidence that can be made an integral part of downstream analysis. Extensive validation of the software and underlying models is planned in three organisms using data from five different validatory experiments. The work proposed in this project will result in significant improvements in the analyses of *-seq data. If successful, this project will replace a host of mapping algorithms, peak callers, and transcript quantifiers, forming the foundation of a software suite for the integrative analysis of *-seq assays.