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Zhou, Wanding; Johnson, Benjamin K; Morrison, Jacob; Beddows, Ian; Eapen, James; Katsman, Efrat; Semwal, Ayush; Habib, Walid Abi; Heo, Lyong; Laird, Peter W; Berman, Benjamin P; Triche, Timothy J; Shen, Hui
Nucleic acids research, 2024-Apr-12, 2024-04-12, 20240412, Letnik: 52, Številka: 6Journal Article
Abstract Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT’s performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing. Graphical Abstract Graphical Abstract
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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in: SICRIS
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