Query Regarding getting same value for start and end position, "DNA methylation"
1 answer
genomation is based on GenomicRanges which uses 1-based coordinates. Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Since a single CpG has a length of 1 you would get the same start and end for a single nucleotide, like chr1-1-1 so on chromosome 1 starting and ending at the first base.
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Your question lacks precision, we do not know what you are talking about
Are you working on bisulphite kind of data or chipseq ????
That's a comment, not an answer, please use
ADD COMMENT.yes I am working on Bisulphate sequenced data.
Yes, that is what methylkit is for. See my answer.