I am learning how to conduct a methylome analysis, and ended reading this from a document entitled "Standards and Guidelines for Whole Genome Shotgun Bisulfite Sequencing"
Sequencing depth. A full DNA methylome should have at least 30X coverage of the genome when reads from biological replicates are combined. For example, a methylome with 2 biological replicates, each with 15X coverage, would be sufficient. Due to strand specificity of bisulfite sequencing data, 30X coverage is equivalent to 15X per strand of the genome. In addition to genome coverage, the average coverage of CpGs may be a useful measure for sequencing depth.
I want to run a general methylome analysis between two conditions: an immature and a mature fruit from a plant with a small genome size.
I am planning to run two biological replicates for each condition, thus a total of 4 BS-Seq will be performed. Each individual BS-Seq can provide 20X coverage. If the former paragraph is true, this will lead to a 40X total coverage for each condition (mature and immature), which is higher and thus better than the minimum and recommended 30X
Any thoughts?
Any ideas?
Am I doing right?
