Title |
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation
|
---|---|
Published in |
Genome Biology, October 2012
|
DOI | 10.1186/gb-2012-13-10-r82 |
Pubmed ID | |
Authors |
Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung |
Abstract |
ABSTRACT: DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United Kingdom | 2 | 29% |
United States | 1 | 14% |
Germany | 1 | 14% |
Canada | 1 | 14% |
Sao Tome and Principe | 1 | 14% |
Japan | 1 | 14% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 3 | 43% |
Members of the public | 2 | 29% |
Science communicators (journalists, bloggers, editors) | 1 | 14% |
Practitioners (doctors, other healthcare professionals) | 1 | 14% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 7 | 5% |
United Kingdom | 2 | 2% |
India | 2 | 2% |
Germany | 1 | <1% |
Sweden | 1 | <1% |
France | 1 | <1% |
Belgium | 1 | <1% |
New Zealand | 1 | <1% |
Japan | 1 | <1% |
Other | 1 | <1% |
Unknown | 110 | 86% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 46 | 36% |
Student > Ph. D. Student | 24 | 19% |
Professor | 10 | 8% |
Student > Master | 9 | 7% |
Professor > Associate Professor | 8 | 6% |
Other | 20 | 16% |
Unknown | 11 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 69 | 54% |
Biochemistry, Genetics and Molecular Biology | 25 | 20% |
Computer Science | 10 | 8% |
Medicine and Dentistry | 4 | 3% |
Mathematics | 2 | 2% |
Other | 6 | 5% |
Unknown | 12 | 9% |