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DNA Modification Patterns Filtering and Analysis Using DNAModAnnot.

Alexis Hardy¹, Sandra Duharcourt², Matthieu Defrance³

¹Université Libre de Bruxelles, Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium.

Methods in Molecular Biology (Clifton, N.J.)

|February 1, 2023

Summary

This summary is machine-generated.

This study introduces a linear workflow for analyzing DNA modifications using the DNAModAnnot package. It enables accurate base-level genome mapping from long-read sequencing data, improving epigenome analysis.

Keywords:

DNA Methylation DNA modifications DNAModAnnot Epigenome Annotation Epigenomics Nanopore technology PacBio Sequencing

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Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Advances in sequencing technologies enable base-resolution genome-wide DNA modification mapping.
Long-read sequencing data (PacBio, ONT) can identify modified base patterns.
Downstream analysis requires genomic annotation and filtering to mitigate artifact signals.

Purpose of the Study:

To present a linear workflow for comprehensive DNA modification analysis.
To introduce the DNA Modification Annotation (DNAModAnnot) package.
To provide a protocol adaptable for annotating epigenomes across organisms.

Main Methods:

Developed a linear workflow utilizing the DNAModAnnot package.
Integrated thorough filtering based on sequencing quality and false discovery rate estimation.
Provided an Rmarkdown script with an application example using PacBio data.

Main Results:

The workflow enables a global analysis of DNA modifications.
Demonstrated application with PacBio data, detailing expected outputs.
Offers guidance for adapting the protocol to various organisms.

Conclusions:

The DNAModAnnot package and workflow facilitate robust analysis of DNA modification patterns.
The presented protocol enhances the accuracy and scope of epigenome annotation.
This approach supports diverse epigenomic research by enabling organism-specific adaptations.