期刊
GENOME BIOLOGY
卷 22, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-021-02349-4
关键词
-
资金
- National Institute of General Medical Sciences [GM128635, GM128636, GM008136, LM012416, GM007267]
PEPPRO is a comprehensive and scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data, producing uniformly processed output files for downstream analysis and assessing data quality.
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.
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