A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing

Wang, X., Yu, X., Zhu, W., McCombie, W. R., Antoniou, E., Powers, R. S., Davidson, N. O., Li, E., Williams, J. (2015) A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics, 31 (12). pp. 2040-2042. ISSN 1367-4803

URL: http://www.ncbi.nlm.nih.gov/pubmed/25681254
DOI: 10.1093/bioinformatics/btv089

Abstract

SUMMARY: 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: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html https://github.com/xfwang/BStools CONTACT: xuefeng.wang@stonybrook.edu SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

Item Type: Paper
Subjects: Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > McCombie lab
CSHL labs > Powers lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: Matt Covey
Date Deposited: 01 Jul 2015 19:13
Last Modified: 05 Nov 2015 15:45
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31608

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