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

Overview of attention for article published in BMC Genomics, January 2015
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Title
Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data
Published in
BMC Genomics, January 2015
DOI 10.1186/1471-2164-16-s11-s2
Pubmed ID
Authors

Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang

Abstract

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. 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. The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 5%
Unknown 20 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 29%
Researcher 5 24%
Student > Bachelor 3 14%
Student > Master 2 10%
Other 1 5%
Other 2 10%
Unknown 2 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 7 33%
Biochemistry, Genetics and Molecular Biology 6 29%
Computer Science 3 14%
Nursing and Health Professions 1 5%
Immunology and Microbiology 1 5%
Other 1 5%
Unknown 2 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 19 November 2015.
All research outputs
#5,618,831
of 6,585,900 outputs
Outputs from BMC Genomics
#4,639
of 5,175 outputs
Outputs of similar age
#196,420
of 248,316 outputs
Outputs of similar age from BMC Genomics
#386
of 408 outputs
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