RNA modification mapping with JACUSA2

• Verfasst von: Piechotta, Michael [VerfasserIn]
• Verfasst von: Naarmann-de Vries, Isabel S. [VerfasserIn]
• Verfasst von: Wang, Qi [VerfasserIn]
• Verfasst von: Altmüller, Janine [VerfasserIn]
• Verfasst von: Dieterich, Christoph [VerfasserIn]
• Titel: RNA modification mapping with JACUSA2
• Verf.angabe: Michael Piechotta, Isabel S. Naarmann-de Vries, Qi Wang, Janine Altmüller and Christoph Dieterich
• E-Jahr: 2022
• Jahr: 16 May 2022
• Umfang: 11 S.
• Fussnoten: Gesehen am 24.06.2022
• Titel Quelle: Enthalten in: Genome biology
• Ort Quelle: London : BioMed Central, 2000
• Jahr Quelle: 2022
• Band/Heft Quelle: 23(2022), Artikel-ID 115, Seite 1-11
• ISSN Quelle: 1474-760X
• DOI: doi:10.1186/s13059-022-02676-0
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: m6A
• Sach-SW: Nanopore
• Sach-SW: Pseudouridine
• Sach-SW: Reverse transcription signature
• K10plus-PPN: 1807739422
• K10plus-PPN:
  Universitätsbibliothek
• Lokale URL UB: Zum Volltext

Abstract

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.