TAMeBS: A sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis
Cytosine methylation plays an important role in many biological regulation processes. The current gold-standard method for analyzing cytosine methylation is based on sodium bisulfite treatment and high-throughput sequencing technologies. In this paper we introduce a new tool called TAMeBS for cytosi...
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| Main Authors: | , , |
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| Other Authors: | |
| Format: | Conference or Workshop Item |
| Language: | English |
| Published: |
2015
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/81227 http://hdl.handle.net/10220/39171 |
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| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | Cytosine methylation plays an important role in many biological regulation processes. The current gold-standard method for analyzing cytosine methylation is based on sodium bisulfite treatment and high-throughput sequencing technologies. In this paper we introduce a new tool called TAMeBS for cytosine methylation analysis using bisulfite sequencing data. It aims to align long bisulfite-treated DNA reads onto a reference genome sequence with high mapping efficiency and estimate the methylation status of each cytosine very accurately. Our approach builds on recent advances in alignment techniques, including bidirectional FM-index, approximate seeds, and the likelihood-ratio scoring matrix which was designed particularly for aligning bisulfite-treated DNA reads. We compared TAMeBS with several popular bisulfite-treated read mapping tools on both simulation and real data. Experimental results showed that TAMeBS could detect many more uniquely best mapped reads than other tested tools while achieving a good balance between sensitivity and precision. The source code of TAMeBS is freely available at https://sourceforge.net/projects/tamebs/. |
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