{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T11:00:50Z","timestamp":1777287650263,"version":"3.51.4"},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771445"],"award-info":[{"award-number":["31771445"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Students' Platform for Innovation and Entrepreneurship Training Program","award":["201810542018"],"award-info":[{"award-number":["201810542018"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>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.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Here we provide a computational method named \u201cBCREval\u201d 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&gt;\u200999.5% 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\u2009&lt;\u20090.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571\u20131572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>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.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-3334-z","type":"journal-article","created":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T16:03:51Z","timestamp":1580486631000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS"],"prefix":"10.1186","volume":"21","author":[{"given":"Junhua","family":"Zhou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minqiong","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zefang","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feilong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yucong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianghua","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zuping","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quanze","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2732-2486","authenticated-orcid":false,"given":"Quanyuan","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"issue":"17","key":"3334_CR1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks454","volume":"40","author":"F Miura","year":"2012","unstructured":"Miura F, Enomoto Y, Dairiki R, Ito T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 2012;40(17):e136. https:\/\/doi.org\/10.1093\/nar\/gks454.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"3334_CR2","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1038\/nbt.1682","volume":"28","author":"RA Harris","year":"2010","unstructured":"Harris RA, Wang T, Coarfa C, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010;28(10):1097\u2013105. https:\/\/doi.org\/10.1038\/nbt.1682.","journal-title":"Nat Biotechnol"},{"issue":"10","key":"3334_CR3","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nbt1010-1045","volume":"28","author":"BE Bernstein","year":"2010","unstructured":"Bernstein BE, Stamatoyannopoulos JA, Costello JF, et al. The NIH roadmap Epigenomics mapping Consortium. Nat Biotechnol. 2010;28(10):1045\u20138. https:\/\/doi.org\/10.1038\/nbt1010-1045.","journal-title":"Nat Biotechnol"},{"issue":"7414","key":"3334_CR4","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"TEP Consortium","year":"2012","unstructured":"Consortium TEP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57\u201374. https:\/\/doi.org\/10.1038\/nature11247.","journal-title":"Nature."},{"issue":"3","key":"3334_CR5","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/nbt.2153","volume":"30","author":"D Adams","year":"2012","unstructured":"Adams D, Altucci L, Antonarakis SE, et al. BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012;30(3):224\u20136. https:\/\/doi.org\/10.1038\/nbt.2153.","journal-title":"Nat Biotechnol"},{"key":"3334_CR6","unstructured":"The International Human Epigenome Consortium. 2016. http:\/\/ihec-epigenomes.org\/."},{"issue":"2","key":"3334_CR7","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1038\/nmeth.1828","volume":"9","author":"F Krueger","year":"2012","unstructured":"Krueger F, Kreck B, Franke A, Andrews SR. DNA methylome analysis using short bisulfite sequencing data. Nat Methods. 2012;9(2):145\u201351. https:\/\/doi.org\/10.1038\/nmeth.1828.","journal-title":"Nat Methods"},{"issue":"11","key":"3334_CR8","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","volume":"27","author":"F Krueger","year":"2011","unstructured":"Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btr167.","journal-title":"Bioinformatics."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3334-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-3334-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3334-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,30]],"date-time":"2021-01-30T00:10:28Z","timestamp":1611965428000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3334-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,31]]},"references-count":8,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3334"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-3334-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,31]]},"assertion":[{"value":"26 March 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 December 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"38"}}