title: A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.
abstract: Currently available bisulfite sequencing tools frequently suffer from low mapping rates and low methylation calls, especially for data generated from the Illumina sequencer, NextSeq. Here, we introduce a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is implemented in an automated analysis toolkit for processing bisulfite sequencing reads.
  
  
  METHODS
  http://mysbfiles.stonybrook.edu/~xuefenwang/software.html and https://github.com/xfwang/BStools.
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Xuefeng
authors: X
authors: Wang
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Xiaoqing
authors: X
authors: Yu
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Wei
authors: W
authors: Zhu
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: W Richard
authors: WR
authors: McCombie
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Eric
authors: E
authors: Antoniou
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: R Scott
authors: RS
authors: Powers
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Nicholas O
authors: NO
authors: Davidson
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Ellen
authors: E
authors: Li
authors: Department of Preventive Medicine, Department of Biomedical Informatics, and Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, Department of Biostatistics, Yale University, New Haven, CT 06520, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, Department of Medicine, Washington University St Louis, St Louis, MO 63110 and Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Jennie
authors: J
authors: Williams
mesh_terms: D019175:DNA Methylation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite