Query Regarding getting same value for start and end position, "DNA methylation"

Question

[Pankaj]

Hi everyone,

Greetings!

While using methyl kit for Bisulphate sequenced data, I am getting similar start and end positions. Please help me to find a way to get different start and end positions.

Thank you in anticipation.

[Basti]

Your question lacks precision, we do not know what you are talking about

[bioinfo_ga]

Are you working on bisulphite kind of data or chipseq ????

[ATpoint]

That's a comment, not an answer, please use ADD COMMENT.

[Pankaj]

yes I am working on Bisulphate sequenced data.

[ATpoint]

Yes, that is what methylkit is for. See my answer.

Answer 1

[ATpoint]

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.