BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS Article Swipe
Junhua Zhou
,
Minqiong Zhao
,
Zefang Sun
,
Feilong Wu
,
Yucong Liu
,
Xiang-hua Liu
,
Zuping He
,
Quanze He
,
Quanyuan He
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1186/s12859-019-3334-z
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1186/s12859-019-3334-z
Background Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethylated cytosines into thymines (BS conversion). Incomplete conversion of unmethylated cytosines can introduce false positive methylation call. Developing a quick method to evaluate bisulfite conversion ratio (BCR) is benefit for both quality control and data analysis of WGBS. Results Here we provide a computational method named “BCREval” to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control. We tested the method by using public WGBS data and found that it is very stable and most of BS conversion assays can achieve> 99.5% efficiency. The non-CpG DNA methylation at telomere fits a binomial model and may result from a random process with very low possibility (the ratio < 0.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571–1572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter. Conclusion Our method is a simple but robust method to QC and speculates BCR for WGBS experiments to make sure it achieves acceptable level. It is faster and more efficient than current tools and can be easily integrated into presented WGBS pipelines.
Related Topics
Concepts
Bisulfite
Computer science
Computational biology
Biology
Genetics
DNA methylation
Gene
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1186/s12859-019-3334-z
- https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3334-z.pdf
- OA Status
- gold
- Cited By
- 27
- References
- 7
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3007870963
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3007870963Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1186/s12859-019-3334-zDigital Object Identifier
- Title
-
BCREval: a computational method to estimate the bisulfite conversion ratio in WGBSWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-01-31Full publication date if available
- Authors
-
Junhua Zhou, Minqiong Zhao, Zefang Sun, Feilong Wu, Yucong Liu, Xiang-hua Liu, Zuping He, Quanze He, Quanyuan HeList of authors in order
- Landing page
-
https://doi.org/10.1186/s12859-019-3334-zPublisher landing page
- PDF URL
-
https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3334-z.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3334-z.pdfDirect OA link when available
- Concepts
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Bisulfite, Computer science, Computational biology, Biology, Genetics, DNA methylation, Gene, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
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27Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 5, 2023: 13, 2022: 4, 2021: 3Per-year citation counts (last 5 years)
- References (count)
-
7Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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