An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
Abstract Background DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution. However, genomic variations such as insertions and dele...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2593-4 |
| _version_ | 1818806920088125440 |
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| author | Qiangwei Zhou Jing-Quan Lim Wing-Kin Sung Guoliang Li |
| author_facet | Qiangwei Zhou Jing-Quan Lim Wing-Kin Sung Guoliang Li |
| author_sort | Qiangwei Zhou |
| collection | DOAJ |
| description | Abstract Background DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution. However, genomic variations such as insertions and deletions (indels) affect methylation calling, and the alignment of reads near/across indels becomes inaccurate in the presence of polymorphisms. Hence, the simultaneous detection of DNA methylation and indels is important for exploring the mechanisms of functional regulation in organisms. Results These problems motivated us to develop the algorithm BatMeth2, which can align BS reads with high accuracy while allowing for variable-length indels with respect to the reference genome. The results from simulated and real bisulfite DNA methylation data demonstrated that our proposed method increases alignment accuracy. Additionally, BatMeth2 can calculate the methylation levels of individual loci, genomic regions or functional regions such as genes/transposable elements. Additional programs were also developed to provide methylation data annotation, visualization, and differentially methylated cytosine/region (DMC/DMR) detection. The whole package provides new tools and will benefit bisulfite data analysis. Conclusion BatMeth2 improves DNA methylation calling, particularly for regions close to indels. It is an autorun package and easy to use. In addition, a DNA methylation visualization program and a differential analysis program are provided in BatMeth2. We believe that BatMeth2 will facilitate the study of the mechanisms of DNA methylation in development and disease. BatMeth2 is an open source software program and is available on GitHub (https://github.com/GuoliangLi-HZAU/BatMeth2/). |
| first_indexed | 2024-12-18T19:17:26Z |
| format | Article |
| id | doaj.art-c9ab00039aa9457689c1aa66a6aab04c |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T19:17:26Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-c9ab00039aa9457689c1aa66a6aab04c2022-12-21T20:56:06ZengBMCBMC Bioinformatics1471-21052019-01-0120111110.1186/s12859-018-2593-4An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mappingQiangwei Zhou0Jing-Quan Lim1Wing-Kin Sung2Guoliang Li3National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural UniversityDepartment of Computer Science, National University of SingaporeDepartment of Computer Science, National University of SingaporeNational Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural UniversityAbstract Background DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution. However, genomic variations such as insertions and deletions (indels) affect methylation calling, and the alignment of reads near/across indels becomes inaccurate in the presence of polymorphisms. Hence, the simultaneous detection of DNA methylation and indels is important for exploring the mechanisms of functional regulation in organisms. Results These problems motivated us to develop the algorithm BatMeth2, which can align BS reads with high accuracy while allowing for variable-length indels with respect to the reference genome. The results from simulated and real bisulfite DNA methylation data demonstrated that our proposed method increases alignment accuracy. Additionally, BatMeth2 can calculate the methylation levels of individual loci, genomic regions or functional regions such as genes/transposable elements. Additional programs were also developed to provide methylation data annotation, visualization, and differentially methylated cytosine/region (DMC/DMR) detection. The whole package provides new tools and will benefit bisulfite data analysis. Conclusion BatMeth2 improves DNA methylation calling, particularly for regions close to indels. It is an autorun package and easy to use. In addition, a DNA methylation visualization program and a differential analysis program are provided in BatMeth2. We believe that BatMeth2 will facilitate the study of the mechanisms of DNA methylation in development and disease. BatMeth2 is an open source software program and is available on GitHub (https://github.com/GuoliangLi-HZAU/BatMeth2/).http://link.springer.com/article/10.1186/s12859-018-2593-4DNA methylationBisulfite sequencingAlignmentIndelPipeline |
| spellingShingle | Qiangwei Zhou Jing-Quan Lim Wing-Kin Sung Guoliang Li An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping BMC Bioinformatics DNA methylation Bisulfite sequencing Alignment Indel Pipeline |
| title | An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping |
| title_full | An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping |
| title_fullStr | An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping |
| title_full_unstemmed | An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping |
| title_short | An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping |
| title_sort | integrated package for bisulfite dna methylation data analysis with indel sensitive mapping |
| topic | DNA methylation Bisulfite sequencing Alignment Indel Pipeline |
| url | http://link.springer.com/article/10.1186/s12859-018-2593-4 |
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