RNA modification mapping with JACUSA2

Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection assays that are based on either the Illumina or Nanopore plat...

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Autores principales: Piechotta, Michael, Naarmann-de Vries, Isabel S., Wang, Qi, Altmüller, Janine, Dieterich, Christoph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9109409/
https://www.ncbi.nlm.nih.gov/pubmed/35578346
http://dx.doi.org/10.1186/s13059-022-02676-0
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author Piechotta, Michael
Naarmann-de Vries, Isabel S.
Wang, Qi
Altmüller, Janine
Dieterich, Christoph
author_facet Piechotta, Michael
Naarmann-de Vries, Isabel S.
Wang, Qi
Altmüller, Janine
Dieterich, Christoph
author_sort Piechotta, Michael
collection PubMed
description Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection assays that are based on either the Illumina or Nanopore platform. Importantly, JACUSA2 can integrate information from multiple experiments, such as replicates and different conditions, and different library types, such as first- or second-strand cDNA libraries. We demonstrate its utility, showing analysis workflows for N6-methyladenosine (m6A) and pseudouridine (Ψ) detection on Illumina and Nanopore sequencing data sets. Our software and its R helper package are available as open source solutions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02676-0).
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spelling pubmed-91094092022-05-17 RNA modification mapping with JACUSA2 Piechotta, Michael Naarmann-de Vries, Isabel S. Wang, Qi Altmüller, Janine Dieterich, Christoph Genome Biol Short Report Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection assays that are based on either the Illumina or Nanopore platform. Importantly, JACUSA2 can integrate information from multiple experiments, such as replicates and different conditions, and different library types, such as first- or second-strand cDNA libraries. We demonstrate its utility, showing analysis workflows for N6-methyladenosine (m6A) and pseudouridine (Ψ) detection on Illumina and Nanopore sequencing data sets. Our software and its R helper package are available as open source solutions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02676-0). BioMed Central 2022-05-16 /pmc/articles/PMC9109409/ /pubmed/35578346 http://dx.doi.org/10.1186/s13059-022-02676-0 Text en © The Author(s) 2022 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 Short Report
Piechotta, Michael
Naarmann-de Vries, Isabel S.
Wang, Qi
Altmüller, Janine
Dieterich, Christoph
RNA modification mapping with JACUSA2
title RNA modification mapping with JACUSA2
title_full RNA modification mapping with JACUSA2
title_fullStr RNA modification mapping with JACUSA2
title_full_unstemmed RNA modification mapping with JACUSA2
title_short RNA modification mapping with JACUSA2
title_sort rna modification mapping with jacusa2
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9109409/
https://www.ncbi.nlm.nih.gov/pubmed/35578346
http://dx.doi.org/10.1186/s13059-022-02676-0
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