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

BMC Genomics

Research

Liqing Zhang¹  Jacob Porter¹  Ming-an Sun²  Hehuang Xie³ 

[1] Department of Computer Science, Virginia Tech, 24061, Blacksburg, VA, USA;Virginia Bioinformatics Institute, Virginia Tech, 24061, Blacksburg, VA, USA;Virginia Bioinformatics Institute, Virginia Tech, 24061, Blacksburg, VA, USA;Department of Biological Sciences, Virginia Tech, 24061, Blacksburg, VA, USA;

关键词: Methylation;    Bisulfite short read mapping;    Next-generation Sequencing;    hairpin bisulfite data;    Sequence Complexity;    Entropy;   

DOI  :  10.1186/1471-2164-16-S11-S2

来源: Springer

【 摘 要 】

BackgroundDNA 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 reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency.ResultsTo address this issue, we used the hairpin bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-bisulfite-converted sequences. We used Bismark for bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy.ConclusionsThe hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

【 授权许可】

Unknown   
© Porter et al.; 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.