I'm just learning how to perform an analysis of methylation patterns using bisulfite sequencing data, but I have some questions:
1. What database I can use for obtain bisulfite sequencing data?
2. I should start performing an analysis focused on one chromosome or on one whole genome?
3. Because I want to perform this type of analysis in the context of cancer epigenomics (specifically methylation patterns of promoters and genes), is it good idea to use RRBS data instead of WGBS data?
Using RRBS data as a first approach might be a good idea. Specially if you wish to analyze methylation patterns in promoter regions. Although, WGBS data could give you more information, the amount of data to be analyzed for each sample is much more compared to RRBS data and the coverage of promoter regions using either RRBS or WGBS should be very similar.
Another thing to consider is the amount of datasets found for each approach.
If computing power is not a problem, I will start analyzing whole genome data instead of specific chromosomes.
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