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PEPPRO: quality control and processing of nascent RNA profiling data.

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.

SUBMITTER: Smith JP

PROVIDER: S-EPMC8126160 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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PEPPRO: quality control and processing of nascent RNA profiling data.

Smith Jason P JP Dutta Arun B AB Sathyan Kizhakke Mattada KM Guertin Michael J MJ Sheffield Nathan C NC

Genome biology 20210515 1

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 ...[more]

PMID: 33992117

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