Bisulfite sequencing analysis
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6.1 years ago
lookamrita • 0

Hi,

I am trying to analyse Whole genome bisulfite sequencing data of Rice, but it is having biological replicates in the samples, which tool is good for this. I am very new to this field and have heard about Bismark, which was for no replicated data. Please tell me about any tool to analyse replicates. 

next-gen WGBS • 1.7k views
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Bismark is an aligner and methylation extractor. Are you asking about alignment (bismark works fine, it's just slow) or the actual analysis, for which bismark isn't used?

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6.1 years ago

Bismark will do the analysis of the methylation state. You need to do it by separate to your samples. This means you need to run Bismark for sure, and then you run the comparison afterwards

Take a look to this WEB Service for methylation analysis. It is slow to run because it must be overcrowded. But try to get the paper in which this service is described to be able to compare this service with the many other programs to analyze methylation, and you will be ending with a relation of useful programs to use

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