Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches
暂无分享,去创建一个
[1] A. C. Mateman,et al. epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing , 2022, Molecular ecology resources.
[2] P. Stadler,et al. EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics , 2021, NAR genomics and bioinformatics.
[3] Eloi Casals,et al. gemBS: high throughput processing for DNA methylation data from bisulfite sequencing , 2018, Bioinform..
[4] Toby Bloom,et al. Whole-genome bisulfite sequencing with improved accuracy and cost , 2018, Genome research.
[5] Karsten M. Borgwardt,et al. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana , 2016, Cell.
[6] Chuan He,et al. Nucleic Acid Modifications in Regulation of Gene Expression. , 2016, Cell chemical biology.
[7] Pengfei Song,et al. BS-SNPer: SNP calling in bisulfite-seq data , 2015, Bioinform..
[8] John G. Cleary,et al. Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines , 2015, bioRxiv.
[9] Matteo Pellegrini,et al. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. , 2014, Molecular cell.
[10] G. McVean,et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.
[11] J. Zook,et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls , 2013, Nature Biotechnology.
[12] Brent S. Pedersen,et al. Fast and accurate alignment of long bisulfite-seq reads , 2014, 1401.1129.
[13] J. Oliver,et al. MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data , 2013, F1000Research.
[14] J. Oliver,et al. MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data. , 2013, F1000Research.
[15] Nathan C. Sheffield,et al. The accessible chromatin landscape of the human genome , 2012, Nature.
[16] Gabor T. Marth,et al. Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.
[17] P. Laird,et al. Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data , 2012, Genome Biology.
[18] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[19] Joseph K. Pickrell,et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines , 2011, Genome Biology.
[20] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[21] Lee E. Edsall,et al. Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.
[22] T. Kakutani,et al. Bursts of retrotransposition reproduced in Arabidopsis , 2009, Nature.
[23] D. Weigel,et al. Selective epigenetic control of retrotransposition in Arabidopsis , 2009, Nature.
[24] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[25] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[26] R. Lister,et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.
[27] S. Nelson,et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning , 2008, Nature.
[28] W. Reik. Stability and flexibility of epigenetic gene regulation in mammalian development , 2007, Nature.
[29] M. Pellegrini,et al. Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis , 2006, Cell.
[30] Hilde van der Togt,et al. Publisher's Note , 2003, J. Netw. Comput. Appl..
[31] Howard Cedar,et al. DNA methylation represses transcription in vivo , 1999, Nature Genetics.