دورية أكاديمية
أعرض في EDS

Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.

التفاصيل البيبلوغرافية
العنوان: Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.
المؤلفون: Wolpe JB; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA., Martins AL; Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT, USA.; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA., Guertin MJ; Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT, USA.; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA.
المصدر: NAR genomics and bioinformatics [NAR Genom Bioinform] 2023 Jun 02; Vol. 5 (2), pp. lqad054. Date of Electronic Publication: 2023 Jun 02 (Print Publication: 2023).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 101756213 Publication Model: eCollection Cited Medium: Internet ISSN: 2631-9268 (Electronic) Linking ISSN: 26319268 NLM ISO Abbreviation: NAR Genom Bioinform Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [Oxford] : Oxford University Press, [2019]-
مستخلص: Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transposase accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods. We model this complex bias using a rule ensemble machine learning approach that integrates information from many input k-mers proximal to the ATAC sequence reads. We effectively characterize and correct single-nucleotide sequence biases and regional sequence biases of the Tn5 enzyme. Correction of enzymatic sequence bias is an important step in interpreting chromatin accessibility assays that aim to infer transcription factor binding and regulatory activity of elements in the genome.
(© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
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معلومات مُعتمدة: R35 GM128635 United States GM NIGMS NIH HHS
تواريخ الأحداث: Date Created: 20230605 Latest Revision: 20230919
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC10236359
DOI: 10.1093/nargab/lqad054
PMID: 37274120
قاعدة البيانات: MEDLINE
الوصف
تدمد:2631-9268
DOI:10.1093/nargab/lqad054