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We cannot get RRBS libraries to work in our lab at all. We have made many regular libraries and many WGBS libraries. I came across something in a Nature 2010 paper that uses methylated dCTP's as well as dGTP's for the blunt ending step of the library prep. We have never used methylated dCTP's in our RRBS tries and I am wondering if this could be the core issue. Can anyone comment on why methylated dCTP's are used. I am wondering if it is for the sake of library prep or just for analysis reasons at the end.
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I worked with RRBS for a while and it was working ok (at least the library prep, we never actually sequenced anything because we then switched to WGS). I don´t have the protocol with me right now, but as far as I remember it shouldn´t matter whether you use mdCTP or not in the end repair step. The important thing is that your adapters are methylated in all the Cs, in order to make sure the PCR pre-amplification primers will bind and amplify the ligated product.
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