title: Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data.
abstract: BACKGROUND
  DNA 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.
  
  
  RESULTS
  To 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.
  
  
  CONCLUSIONS
  The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.
authors.forename: Jacob
authors.initials: J
authors.lastname: Porter
authors.forename: Ming-an
authors.initials: MA
authors.lastname: Sun
authors.forename: Hehuang
authors.initials: H
authors.lastname: Xie
authors.forename: Liqing
authors.initials: L
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D019175:DNA Methylation / Q000187:drug effects; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000494:pharmacology*
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite