RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different algorithms. Furthermore, the analysis consists of several steps regarding alignment (primary-analysis), quantification, differential analysis (secondary-analysis) and any tertiary-analysis and can therefore be time-consuming to deal with each step separately, in addition to requiring a computer knowledge. For this reason, the development of an automated pipeline that allows the entire analysis to be managed through a single initial command and that is easy to use even for those without computer skills can be useful. Faced with the vast availability of RNA-Seq analysis tools, it is first of all necessary to select a limited number of pipelines to include. For this purpose, we compared eight pipelines obtained by combining the most used tools and for each one we evaluated peak of RAM, time, sensitivity and specificity. The pipeline with shorter times, lower consumption of RAM and higher sensitivity is the one consisting in HISAT2 for alignment, featureCounts for quantification and edgeR for differential analysis. Here, we developed ARPIR, an automated pipeline that recurs by default to the cited pipeline, but it also allows to choose, between different tools, those of the pipelines having the best performances. ARPIR allows the analysis of RNA-Seq data from groups undergoing different treatment allowing multiple comparisons in a single launch and can be used either for paired-end or single-end analysis. All the required prerequisites can be installed via a configuration script and the analysis can be launched via a graphical interface or by a template script. In addition, ARPIR makes a final tertiary-analysis that includes a Gene Ontology and Pathway analysis. The results can be viewed in an interactive Shiny App and exported in a report (pdf, word or html formats). ARPIR is an efficient and easy-to-use tool for RNA-Seq analysis from quality control to Pathway analysis that allows you to choose between different pipelines.

中文翻译：

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ARPIR：具有交互式报告的自动RNA-Seq管道

RNA-Seq是用于研究编码和非编码RNA表达的一种越来越常用的方法。RNA-Seq分析的每个阶段都有许多软件工具可用，并且每个工具使用不同的算法。此外，分析包括有关比对（初步分析），定量，差异分析（二次分析）和任何三次分析的几个步骤，因此除了需要计算机外，单独处理每个步骤也很耗时知识。因此，开发一种自动化管道可以使整个分析通过一个初始命令进行管理，即使对于那些没有计算机技能的人也很容易使用，因此很有用。面对大量的RNA-Seq分析工具，首先，必须选择要包含的有限数量的管道。为此，我们比较了通过组合最常用的工具获得的8条流水线，并针对每种流水评估了RAM的峰值，时间，灵敏度和特异性。时间较短，RAM消耗较低，灵敏度更高的管线是由HISAT2进行对齐，由featureCounts进行量化以及edgeR进行差异分析。在这里，我们开发了ARPIR，这是一种自动流水线，默认情况下会重复到引用的流水线，但是它也允许在不同的工具之间选择性能最佳的流水线。ARPIR可以分析经历不同处理的组的RNA-Seq数据，从而允许在一次启动中进行多次比较，并且可以用于双末端或单末端分析。可以通过配置脚本安装所有必需的先决条件，并且可以通过图形界面或模板脚本启动分析。此外，ARPIR进行了最终的第三级分析，其中包括基因本体论和途径分析。可以在交互式Shiny App中查看结果，并以报告（pdf，word或html格式）导出结果。ARPIR是一种高效且易于使用的工具，可用于从质量控制到路径分析的RNA-Seq分析，使您可以在不同的管线之间进行选择。Word或html格式）。ARPIR是一种高效且易于使用的工具，可用于从质量控制到路径分析的RNA-Seq分析，使您可以在不同的管线之间进行选择。Word或html格式）。ARPIR是一种高效且易于使用的工具，可用于从质量控制到路径分析的RNA-Seq分析，使您可以在不同的管线之间进行选择。