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I have a question regarding the noise between biological replicates in bisulfite sequencing experiments. From the papers that I have read, they usually make mention of the number of biological replicates in use (2 in case of the recently published tomato methylome), but they don't, as far as I can tell, mention if there is a great deal of variability in cytosine methylation for a given base. Any information or direction to a paper would be very helpful to me.
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It seems to vary greatly by base and experiment. Check out some of the supplemental figures in this paper, which I recall show some nice methylation level vs. variance graphs.
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