gemBS: high throughput processing for DNA methylation data from bisulfite sequencing
نویسندگان
چکیده
منابع مشابه
DNA Methylation Profiling from High-Throughput Sequencing Data
The methylation of a cytosine at the carbon 5 position (5meC) is a common epigenetic mark in eukaryotic cells that is normally found in CpG and CpHpG (H=A,C,T) sequence contexts. The inactivation of one of the X-chromosomes in female cells, the allele-specific expression of imprinted genes or the role in the embryonic development which is shown by the early lethality of Dnmt3a and Dnmt3b defici...
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High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure. However, methods for large-scale identification of methylation patterns from bisulfite sequencing are lacking. We developed a comprehensive tool, CpG...
متن کاملBiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
Bisulfite sequencing is a widely used method for measuring DNA methylation in eukaryotic genomes. The assay provides single-base pair resolution and, given sufficient sequencing depth, its quantitative accuracy is excellent. High-throughput sequencing of bisulfite-converted DNA can be applied either genome wide or targeted to a defined set of genomic loci (e.g. using locus-specific PCR primers ...
متن کاملBiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
SUMMARY Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for this process. In an easy-to-use manner, the tool helps the user to import the sequence files from the sequencer, to align them, to exclude or correct critical sequences, to document the experiment, to p...
متن کاملQuantification of DNA Methylation and Epimutations from Bisulfite Sequencing Data – the BEAT package
The following example illustrates a standard use case of the BEAT package, which is used for processing and modeling methylated and unmethylated counts of CG positions from Bisulfite sequencing (BS-Seq) for determination of epimutation rates, i.e. the rate of change in DNA methylation status at CG sites between a reference multi-cell sample and single-cell samples. The input for the package BEA...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2018
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bty690