Xuefeng Wang1, Xiaoqing Yu2, Wei Zhu2, W Richard McCombie2, Eric Antoniou2, R Scott Powers3, Nicholas O Davidson2, Ellen Li2, Jennie Williams2. 1. 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. 2. 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. 3. 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.
Abstract
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html and https://github.com/xfwang/BStools.
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html and https://github.com/xfwang/BStools.
Authors: Xuefeng Wang; Ping Ji; Yuanhao Zhang; Joseph F LaComb; Xinyu Tian; Ellen Li; Jennie L Williams Journal: PLoS One Date: 2016-04-25 Impact factor: 3.240