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Article Dans Une Revue Methods in Molecular Biology Année : 2023

DNA Modification Patterns Filtering and Analysis Using DNAModAnnot

Résumé

Mapping DNA modifications at the base resolution is now possible at the genome level thanks to advances in sequencing technologies. Long-read sequencing data can be used to identify modified base patterns. However, the downstream analysis of Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data requires the integration of genomic annotation and comprehensive filtering to prevent the accumulation of artifact signals. We present in this chapter, a linear workflow to fully analyze modified base patterns using the DNA Modification Annotation (DNAModAnnot) package. This workflow includes a thorough filtering based on sequencing quality and false discovery rate estimation and provides tools for a global analysis of DNA modifications. Here, we provide an application example of this workflow with PacBio data and guide the user by explaining expected outputs via a fully integrated Rmarkdown script. This protocol is presented with tips showing how to adapt the provided code for annotating epigenomes of any organism according to the user needs.
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Dates et versions

hal-04240829 , version 1 (27-06-2024)

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Alexis Hardy, Sandra Duharcourt, Matthieu Defrance. DNA Modification Patterns Filtering and Analysis Using DNAModAnnot. Methods in Molecular Biology, 2023, Computational Epigenomics and Epitranscriptomics, 2624, pp.87-114. ⟨10.1007/978-1-0716-2962-8_7⟩. ⟨hal-04240829⟩
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