PEPPRO: quality control and processing of nascent RNA profiling data
Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Abstract
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.
Topics & Concepts
WorkflowBiologyComputational biologyRNARNA-SeqProfiling (computer programming)Adapter (computing)Computer scienceData miningDatabaseGeneticsTranscriptomeGeneOperating systemGene expressionGenomics and Phylogenetic StudiesRNA modifications and cancerCancer-related molecular mechanisms research