BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation
Jing Quan Lim,Chandana Tennakoon,Guoliang Li,Eleanor Wong,Eleanor Wong,Yijun Ruan,Chia-Lin Wei,Chia-Lin Wei,Wing-Kin Sung,Wing-Kin Sung +9 more
TLDR
BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatches Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision.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/.read more
Citations
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Journal ArticleDOI
Identification and analysis of adenine N6-methylation sites in the rice genome.
Chao Zhou,Changshi Wang,Hongbo Liu,Qiangwei Zhou,Qian Liu,Yan Guo,Ting Peng,Jiaming Song,Jianwei Zhang,Ling-Ling Chen,Yu Zhao,Zhixiong Zeng,Dao-Xiu Zhou,Dao-Xiu Zhou +13 more
TL;DR: A map of N6-methyladenine in the rice genome is provided, its association with gene expression and 5-methylcytosine is examined and a potential demethylase for this epigenomic mark is reported.
Journal ArticleDOI
DMAP: differential methylation analysis package for RRBS and WGBS data
TL;DR: A novel fragment-based approach for investigating DNA methylation patterns for reduced representation bisulphite sequencing data is introduced and DMAP provides the identity of gene and CpG features and distances to the differentially methylated regions in a format that is easily analyzed with limited bioinformatics knowledge.
Journal ArticleDOI
Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways
TL;DR: The function of OsDDM1 and OsDRM2 defines distinctDNA methylation pathways in the bulk of DNA methylation of the genome, which is possibly related to the dispersed heterochromatin across chromosomes in rice and suggests that DNA methylations mechanisms may vary among different plant species.
Journal ArticleDOI
The Chinese pine genome and methylome unveil key features of conifer evolution
TL;DR: Wang et al. as mentioned in this paper presented a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content.
Journal ArticleDOI
Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions
TL;DR: Bisulfighter is presented, a new software package for detecting mCs and DMRs from bisulfite sequencing data that combines the LAST alignment tool for mC calling, and a novel framework for DMR detection based on hidden Markov models (HMMs).
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