Titlebook: Computational Epigenomics and Epitranscriptomics; Pedro H. Oliveira Book 2023 The Editor(s) (if applicable) and The Author(s), under exclu

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Pseudouridine Identification and Functional Annotation with PIANO,gical processes. Accurately identifying the location of Ψ sites is helpful for relevant downstream researches. In this chapter, we introduce a website PIANO—for .seudouridine site (Ψ) .dentification .nd fu.ctional ann.tation, which enables researchers to predict human putative Ψ sites with a high-ac

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Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores,data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible data analysis in transcriptomic and epitranscriptomic studies. We introduce the key concepts of MoP2 and provide a step-by-step fully reproducible and complete example of how to use the workflow for

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,Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq,nce was reported in tRNA, rRNA, and sn/snoRNA as well as in mRNA/lncRNA. Multiple analytical deep sequencing-based approaches have been proposed for pseudouridine detection and quantification, among which the most popular relies on the use of soluble carbodiimide (termed CMCT). Recently, we develope

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Sequoia: A Framework for Visual Analysis of RNA Modifications from Direct RNA Sequencing Data, to interactively analyze signals originating from nanopore sequencers and can readily be extended to both RNA and DNA sequencing datasets. Sequoia combines a Python-based backend with a multi-view graphical interface that allows users to ingest raw nanopore sequencing data in Fast5 format, cluster

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Mapping of RNA Modifications by Direct Nanopore Sequencing and JACUSA2,o a sample lacking a specific modification type (e.g., “knockout” sample, here .-KO) or . a sample of interest with modifications is compared to a sample lacking all modifications (e.g., in vitro transcribed cDNA). We provide a detailed protocol on experimental and computational aspects. Extensive o

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