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Sci Rep. 2018 Feb 1;8(1):2190. doi: 10.1038/s41598-018-19655-w.

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

Author information

1
Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia. benjamin.mayne@adelaide.edu.au.
2
Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia. benjamin.mayne@adelaide.edu.au.
3
Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.
4
Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.
5
Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
6
Plant Energy Biology, ARC Centre of Excellence, The University of Western Australia, Perth, WA, 6009, Australia.
7
Environmental Epigenetics and Genetics Group, School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
8
Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, 5005, Australia.
9
Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia. jimmy.breen@adelaide.edu.au.
10
Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia. jimmy.breen@adelaide.edu.au.

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 ).

PMID:
29391490
PMCID:
PMC5794748
DOI:
10.1038/s41598-018-19655-w
[Indexed for MEDLINE]
Free PMC Article

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