Cargando…

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitat...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kunde-Ramamoorthy, Govindarajan, Coarfa, Cristian, Laritsky, Eleonora, Kessler, Noah J., Harris, R. Alan, Xu, Mingchu, Chen, Rui, Shen, Lanlan, Milosavljevic, Aleksandar, Waterland, Robert A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973287/ https://www.ncbi.nlm.nih.gov/pubmed/24391148 http://dx.doi.org/10.1093/nar/gkt1325

Ejemplares similares

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
por: Miura, Fumihito, et al.
Publicado: (2012)

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data
por: Scott, C. Anthony, et al.
Publicado: (2020)

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
por: Miura, Fumihito, et al.
Publicado: (2019)

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data
por: Benoukraf, Touati, et al.
Publicado: (2013)

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes
por: Wulfridge, Phillip, et al.
Publicado: (2019)

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
por: Ivanov, Maxim, et al.
Publicado: (2013)

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
por: Wu, Hao, et al.
Publicado: (2015)

A polymerase engineered for bisulfite sequencing
por: Millar, Doug, et al.
Publicado: (2015)

RNA cytosine methylation analysis by bisulfite sequencing
por: Schaefer, Matthias, et al.
Publicado: (2009)

Partial bisulfite conversion for unique template sequencing
por: Kumar, Vijay, et al.
Publicado: (2018)

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms
por: Leakey, Tatiana I., et al.
Publicado: (2008)

Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies
por: Genereux, Diane P., et al.
Publicado: (2008)

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing
por: Lee, Eun-Joon, et al.
Publicado: (2011)

A mostly traditional approach improves alignment of bisulfite-converted DNA
por: Frith, Martin C., et al.
Publicado: (2012)

A new method for accurate assessment of DNA quality after bisulfite treatment
por: Ehrich, Mathias, et al.
Publicado: (2007)

BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes
por: Tusnády, Gábor E., et al.
Publicado: (2005)

Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing
por: Giehr, Pascal, et al.
Publicado: (2018)

Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR
por: Yang, Inchul, et al.
Publicado: (2006)

Early Postnatal Nutrition Determines Adult Physical Activity and Energy Expenditure in Female Mice
por: Li, Ge, et al.
Publicado: (2013)

A ligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA
por: Dahl, Christina, et al.
Publicado: (2007)

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM
por: Fong, Jerry, et al.
Publicado: (2021)

Whole-genome bisulfite sequencing with improved accuracy and cost
por: Suzuki, Masako, et al.
Publicado: (2018)

Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA
por: Tetzner, Reimo, et al.
Publicado: (2007)

Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns
por: Gravina, Silvia, et al.
Publicado: (2015)

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
por: Han, Lin, et al.
Publicado: (2017)

Bisulfite sequencing Data Presentation and Compilation (BDPC) web server—a useful tool for DNA methylation analysis
por: Rohde, Christian, et al.
Publicado: (2008)

Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform
por: Brena, Romulo Martin, et al.
Publicado: (2006)

MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects
por: Pardo, Carolina E., et al.
Publicado: (2011)

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data
por: Su, Jianzhong, et al.
Publicado: (2013)

Base-resolution detection of N(4)-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing
por: Yu, Miao, et al.
Publicado: (2015)

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
por: Adey, Andrew, et al.
Publicado: (2012)

Laser capture microdissection–reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse
por: Schillebeeckx, Maximiliaan, et al.
Publicado: (2013)

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
por: Hansen, Kasper D, et al.
Publicado: (2012)

Sequence verification of synthetic DNA by assembly of sequencing reads
por: Wilson, Mandy L., et al.
Publicado: (2013)

High-throughput, cost-effective verification of structural DNA assembly
por: Dharmadi, Yandi, et al.
Publicado: (2014)

Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework
por: Li, Miaoxin, et al.
Publicado: (2017)

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool
por: Yu, Haiyuan, et al.
Publicado: (2007)

Rapid, robust plasmid verification by de novo assembly of short sequencing reads
por: Gallegos, Jenna E, et al.
Publicado: (2020)

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
por: Vincent, Martin, et al.
Publicado: (2017)

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs
por: Legrand, Carine, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_86kgdin6v6besrrj80cpuka0q9