Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays

Qiang Jing, Andrew McLellan, John M. Greally, Masako Suzuki

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Abstract

A novel DNA methylation assay, HELP-tagging, has been recently described to use massively parallel sequencing technology for genome-wide methylation profiling. Massively parallel sequencing-based assays such as this produce substantial amounts of data, which complicate analysis and necessitate the use of significant computational resources. To simplify the processing and analysis of HELP-tagging data, a bioinformatic analytical pipeline was developed. Quality checks are performed on the data at various stages, as they are processed by the pipeline to ensure the accuracy of the results. A quantitative methylation score is provided for each locus, along with a confidence score based on the amount of information available for determining the quantification. HELP-tagging analysis results are supplied in standard file formats (BED and WIG) that can be readily examined on the UCSC genome browser.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages79-87
Number of pages9
Volume815
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume815
ISSN (Print)10643745

Fingerprint

High-Throughput Nucleotide Sequencing
DNA Fingerprinting
DNA Methylation
Methylation
Genome
Computational Biology
Technology

Keywords

  • Bioinformatics
  • Computational analysis
  • DNA methylation
  • Pipeline

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Jing, Q., McLellan, A., Greally, J. M., & Suzuki, M. (2012). Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. In Methods in Molecular Biology (Vol. 815, pp. 79-87). (Methods in Molecular Biology; Vol. 815). https://doi.org/10.1007/978-1-61779-424-7_7

Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. / Jing, Qiang; McLellan, Andrew; Greally, John M.; Suzuki, Masako.

Methods in Molecular Biology. Vol. 815 2012. p. 79-87 (Methods in Molecular Biology; Vol. 815).

Research output: Chapter in Book/Report/Conference proceedingChapter

Jing, Q, McLellan, A, Greally, JM & Suzuki, M 2012, Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. in Methods in Molecular Biology. vol. 815, Methods in Molecular Biology, vol. 815, pp. 79-87. https://doi.org/10.1007/978-1-61779-424-7_7
Jing Q, McLellan A, Greally JM, Suzuki M. Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. In Methods in Molecular Biology. Vol. 815. 2012. p. 79-87. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-424-7_7
Jing, Qiang ; McLellan, Andrew ; Greally, John M. ; Suzuki, Masako. / Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. Methods in Molecular Biology. Vol. 815 2012. pp. 79-87 (Methods in Molecular Biology).
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