BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.
BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.
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DOI：
10.1186/1471-2164-13-s8-s9
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Liang H
中科院分区：
文献类型：
--
作者：
Yuan Y;Norris C;Xu Y;Tsui KW;Ji Y;Liang H
RNA测序（RNA-seq）已成为生物医学研究的主要工具。分析RNA-seq数据的一个关键步骤是推断源基因组中短读段的起源，为此，已经开发了许多读段比对/作图软件程序。通常，大多数可定位的读段可以定位到一个明确的基因组位置，并且这些读段被称为独特读段。然而，相当大比例的可映射读段可以与具有相同或相似的同源性的多于一个基因组位置比对，并且它们被称为“多读段”。分配这些多读段具有挑战性，但对于解释RNA-seq数据至关重要。我们最近开发了一种贝叶斯随机模型，它比其他方法更准确地分配多读段（Ji et al. Biometrics 2011）。为了服务于更大的生物社区，我们在一个独立的，高效的，用户友好的软件包BM-Map中实现了这种方法。BM-Map以最流行的读段比对格式SAM（序列比对/地图）作为标准输入;然后基于贝叶斯模型，计算竞争基因组位点的多读段的映射概率; BM-Map通过将映射概率添加到原始SAM文件中来生成输出，以便用户可以轻松进行下游分析。该程序可在三个常见的操作系统，Linux，Mac和PC。此外，我们还建立了一个专门的网站，http：//bioinformatics.mdanderson.org/main/BM-Map，其中包括免费下载，详细的教程和插图示例。我们已经开发了一个独立的，高效的，用户友好的软件包，用于准确分配多读，这是我们以前的方法学论文的重要补充。我们相信，这种生物信息学工具将极大地帮助RNA-seq和相关应用在生命科学研究中发挥其全部潜力。
RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignment/mapping software programs have been developed. Usually, the majority of mappable reads can be mapped to one unambiguous genomic location, and these reads are called unique reads. However, a considerable proportion of mappable reads can be aligned to more than one genomic location with the same or similar fidelities, and they are called "multireads". Allocating these multireads is challenging but critical for interpreting RNA-seq data. We recently developed a Bayesian stochastic model that allocates multireads more accurately than alternative methods (Ji et al. Biometrics 2011). In order to serve a greater biological community, we have implemented this method in a stand-alone, efficient, and user-friendly software package, BM-Map. BM-Map takes SAM (Sequence Alignment/Map), the most popular read alignment format, as the standard input; then based on the Bayesian model, it calculates mapping probabilities of multireads for competing genomic loci; and BM-Map generates the output by adding mapping probabilities to the original SAM file so that users can easily perform downstream analyses. The program is available in three common operating systems, Linux, Mac and PC. Moreover, we have built a dedicated website, http://bioinformatics.mdanderson.org/main/BM-Map, which includes free downloads, detailed tutorials and illustration examples. We have developed a stand-alone, efficient, and user-friendly software package for accurately allocating multireads, which is an important addition to our previous methodology paper. We believe that this bioinformatics tool will greatly help RNA-seq and related applications reach their full potential in life science research.