Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
BMC Genomics. 2014 Jun 3;15(1):423. doi: 10.1186/1471-2164-15-423.
miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant amount of computational resources and bioinformatics expertise. Several web based analytical tools have been developed but they are limited to processing one or a pair of samples at time and are not suitable for a large scale study. Lack of flexibility and reliability of these web applications are also common issues.
We developed a Comprehensive Analysis Pipeline for microRNA Sequencing data (CAP-miRSeq) that integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions. According to computational infrastructure, users can install the package locally or deploy it in Amazon Cloud to run samples sequentially or in parallel for a large number of samples for speedy analyses. In either case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. Using well characterized data, we demonstrated the pipeline's superior performances, flexibility, and practical use in research and biomarker discovery.
CAP-miRSeq is a powerful and flexible tool for users to process and analyze miRNA-seq data scalable from a few to hundreds of samples. The results are presented in the convenient way for investigators or analysts to conduct further investigation and discovery.
miRNAs 在正常生理和各种疾病中发挥着关键作用。通过下一代测序（miRNA-seq）进行 miRNA 分析已成为生物研究和生物标志物发现的主要平台。然而，分析 miRNA 测序数据具有挑战性，因为它需要大量的计算资源和生物信息学专业知识。已经开发了几种基于网络的分析工具，但它们一次只能处理一个或一对样本，不适合大规模研究。这些网络应用程序缺乏灵活性和可靠性也是常见问题。
我们开发了一种用于 miRNA 测序数据的综合分析管道（CAP-miRSeq），该管道集成了读取预处理、比对、成熟/前体/新 miRNA 检测和定量、数据可视化、miRNA 编码区变异检测，以及更灵活的实验条件下差异表达分析。根据计算基础设施，用户可以在本地安装软件包，或在 Amazon Cloud 中部署它，以便对大量样本进行顺序或并行运行，从而快速进行分析。在任何一种情况下，都会为所有样本生成摘要和表达报告，以便更轻松地进行质量评估和下游分析。使用经过良好特征描述的数据，我们证明了该管道在研究和生物标志物发现方面具有优越的性能、灵活性和实际用途。
CAP-miRSeq 是一种强大且灵活的工具，适用于处理和分析从几个到数百个样本的 miRNA-seq 数据。结果以方便调查人员或分析师进行进一步调查和发现的方式呈现。
