PEPPRO: quality control and processing of nascent RNA profiling data

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 fo...

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Autores principales: Smith, Jason P., Dutta, Arun B., Sathyan, Kizhakke Mattada, Guertin, Michael J., Sheffield, Nathan C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126160/
https://www.ncbi.nlm.nih.gov/pubmed/33992117
http://dx.doi.org/10.1186/s13059-021-02349-4
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author Smith, Jason P.
Dutta, Arun B.
Sathyan, Kizhakke Mattada
Guertin, Michael J.
Sheffield, Nathan C.
author_facet Smith, Jason P.
Dutta, Arun B.
Sathyan, Kizhakke Mattada
Guertin, Michael J.
Sheffield, Nathan C.
author_sort Smith, Jason P.
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02349-4).
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spelling pubmed-81261602021-05-17 PEPPRO: quality control and processing of nascent RNA profiling data Smith, Jason P. Dutta, Arun B. Sathyan, Kizhakke Mattada Guertin, Michael J. Sheffield, Nathan C. Genome Biol Software 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02349-4). BioMed Central 2021-05-15 /pmc/articles/PMC8126160/ /pubmed/33992117 http://dx.doi.org/10.1186/s13059-021-02349-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Smith, Jason P.
Dutta, Arun B.
Sathyan, Kizhakke Mattada
Guertin, Michael J.
Sheffield, Nathan C.
PEPPRO: quality control and processing of nascent RNA profiling data
title PEPPRO: quality control and processing of nascent RNA profiling data
title_full PEPPRO: quality control and processing of nascent RNA profiling data
title_fullStr PEPPRO: quality control and processing of nascent RNA profiling data
title_full_unstemmed PEPPRO: quality control and processing of nascent RNA profiling data
title_short PEPPRO: quality control and processing of nascent RNA profiling data
title_sort peppro: quality control and processing of nascent rna profiling data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126160/
https://www.ncbi.nlm.nih.gov/pubmed/33992117
http://dx.doi.org/10.1186/s13059-021-02349-4
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