miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.
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DOI：
10.1371/journal.pone.0143066
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Halushka MK
中科院分区：
文献类型：
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作者：
Baras AS;Mitchell CJ;Myers JR;Gupta S;Weng LC;Ashton JM;Cornish TC;Pandey A;Halushka MK
小RNA RNA-seq for microRNA（miRNAs）是一个快速发展的领域，仍然存在创造更好的生物信息学工具来处理这些大型数据集并生成新的有用分析的机会。我们将miRge打造成一种快速、智能的小型RNA-seq解决方案，以高度多路复用的方式处理样本。miRge采用贝叶斯比对方法，由此将读段与定制的成熟miRNA、发夹miRNA、非编码RNA和mRNA序列文库顺序比对。除了每百万读段（RPM）之外，还在原始读段水平上总结miRNA。提供了所有其他RNA种类（tRNA、rRNA、snoRNA、mRNA）的读数，这对于鉴定潜在污染物和优化小RNA纯化策略是有用的。miRge被设计用于最佳地鉴定miRNA isomiR，并采用基于熵的统计测量来鉴定isomiR的差异产生。这使我们能够确定随着干细胞成熟为视网膜色素上皮细胞，isomiRs中的熵降低。相反，我们发现胰腺肿瘤miRNAs与匹配的正常胰腺组织具有相似的熵。在与其他miRNA分析工具（miRExpress 2.0，sRNAbench，omiRAs，miRDeep 2，Chimira，UEA small RNA测序仪）的头对头比较中，miRge更快（4至32倍），并且是每个样本最大对齐miRNA读数的前两种方法之一。此外，miRge对其复用没有固有的限制。miRge能够在52分钟内同时分析100个小RNA-Seq样本，提供所有样本中miRNA表达的综合分析。由于miRge旨在分析单个和多个样本，因此miRge是高通量和低通量用户的理想工具。miRge可在http://atlas.pathology.jhu.edu/baras/miRge.html上免费获得。
Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.