Cargando…

Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data

BACKGROUND: DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence bisulfite treated DNA. The short sequence reads are mapped to the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Porter, Jacob, Sun, Ming-an, Xie, Hehuang, Zhang, Liqing
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652484/ https://www.ncbi.nlm.nih.gov/pubmed/26576456 http://dx.doi.org/10.1186/1471-2164-16-S11-S2

Ejemplares similares

Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools
por: Tran, Hong, et al.
Publicado: (2014)

HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis
por: Sun, Ming-an, et al.
Publicado: (2015)

A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads
por: Tran, Hong, et al.
Publicado: (2016)

Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis
por: Johnson, Zachary, et al.
Publicado: (2022)

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

Direct comparisons of bisulfite pyrosequencing versus targeted bisulfite sequencing
por: King, Dillon E., et al.
Publicado: (2021)

BiSulfite Bolt: A bisulfite sequencing analysis platform
por: Farrell, Colin, et al.
Publicado: (2021)

Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet
por: de Sena Brandine, Guilherme, et al.
Publicado: (2021)

BS Seeker: precise mapping for bisulfite sequencing
por: Chen, Pao-Yang, et al.
Publicado: (2010)

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

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data
por: Hong, Changjin, et al.
Publicado: (2013)

BSMAP: whole genome bisulfite sequence MAPping program
por: Xi, Yuanxin, et al.
Publicado: (2009)

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation
por: Lim, Jing-Quan, et al.
Publicado: (2012)

Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques
por: Döring, Matthias, et al.
Publicado: (2015)

MOABS: model based analysis of bisulfite sequencing data
por: Sun, Deqiang, et al.
Publicado: (2014)

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
por: Manconi, Andrea, et al.
Publicado: (2014)

An effective method to resolve ambiguous bisulfite-treated reads
por: Liu, Mengya, et al.
Publicado: (2021)

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

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
por: Grehl, Claudius, et al.
Publicado: (2020)

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing
por: Huang, Yun, et al.
Publicado: (2010)

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

NGS-based deep bisulfite sequencing
por: Lee, Suman, et al.
Publicado: (2015)

WBSA: Web Service for Bisulfite Sequencing Data Analysis
por: Liang, Fang, et al.
Publicado: (2014)

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

RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
por: Hetzel, Sara, et al.
Publicado: (2021)

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
por: Eagles, Nicholas J., et al.
Publicado: (2023)

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
por: Kunde-Ramamoorthy, Govindarajan, et al.
Publicado: (2014)

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing
por: Chatterjee, Aniruddha, et al.
Publicado: (2013)

Data quality of whole genome bisulfite sequencing on Illumina platforms
por: Raine, Amanda, et al.
Publicado: (2018)

Maximizing ecological and evolutionary insight in bisulfite sequencing data sets
por: Lea, Amanda J., et al.
Publicado: (2017)

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

Targeted bisulfite sequencing of the dynamic DNA methylome
por: Ziller, Michael J., et al.
Publicado: (2016)

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

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
por: Nunn, Adam, et al.
Publicado: (2021)

Methylated DNA is over-represented in whole-genome bisulfite sequencing data
por: Ji, Lexiang, et al.
Publicado: (2014)

Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
por: Lee, Dohoon, et al.
Publicado: (2023)

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
por: Nunn, Adam, et al.
Publicado: (2021)

An integrative approach for efficient analysis of whole genome bisulfite sequencing data
por: Lee, Jong-Hun, et al.
Publicado: (2015)

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
por: Piao, Yongjun, et al.
Publicado: (2021)

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
por: Zhou, Qiangwei, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_235lnmaq2jte9uodhfi0dsvq01