From WGBS-seq to DMR calling and annotation
Hi, friends, I am new in Whole Genome Bisulfite Sequencing (WGBS-seq) analysis. About Differentially Methylated Regions (DMRs) calling, I have read some papers directly using Fisher Test to detect DMRs and there are also some R packages built to do the detection. Do you have any advice on DMR calling? Also for the annotation (genes, transposable elements), any advice on carrying out the annotation? Thanks so much in advance!
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zhengyunchaosky •
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Great! Thank you so much for your advice!
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zhengyunchaosky •
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For DMR calling, you could use (among many packages) methylKit. It has a solid documentation, is actively being maintained, authors respond to issues on Github, and has the option to aggregate CpG counts over user-specified regions in order to call DMRs. Once you have the DMRs, you could use (again among many) annotatR.
Great! Thank you so much for your advice!
You're very welcome.