PEPPRO：新生 RNA 谱数据的质量控制和处理。

Center for Public Health Genomics, University of Virginia, Charlottesville, USA.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA.

Genome Biol. 2021 May 15;22(1):155. doi: 10.1186/s13059-021-02349-4.

Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPRO produces uniformly processed output files for downstream analysis and assesses adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency. PEPPRO is restartable and fault-tolerant, records copious logs, and provides a web-based project report. PEPPRO can be run locally or using a cluster, providing a portable first step for genomic nascent RNA analysis.

新生 RNA 分析越来越受欢迎；然而，目前还没有标准的分析流程来统一处理数据并评估质量。在这里，我们介绍了 PEPPRO，这是一个用于 GRO-seq、PRO-seq 和 ChRO-seq 数据的全面、可扩展的工作流程。PEPPRO 为下游分析生成统一处理的输出文件，并评估接头丰度、RNA 完整性、文库复杂度、新生 RNA 纯度和运行效率。PEPPRO 可重新启动且容错，记录大量日志，并提供基于网络的项目报告。PEPPRO 可以在本地运行或使用集群运行，为基因组新生 RNA 分析提供了一个可移植的第一步。