MsgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data

Benjamin T. Mayne, Shalem Y. Leemaqz, Sam Buckberry, Carlos M. Rodriguez Lopez, Claire T. Roberts, Tina Bianco-Miotto, James Breen

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/msgbsR.html).

Original languageEnglish
Article number2190
Number of pages8
JournalScientific Reports
Volume8
DOIs
Publication statusPublished - 1 Feb 2018
Externally publishedYes

Bibliographical note

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

Fingerprint Dive into the research topics of 'MsgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data'. Together they form a unique fingerprint.

Cite this