Hi! I wonder some details about the calculation of bisulfite conversion rates.
- It seems that conversion rate can be calculated using all types of C ( CpG, CHH, CHG ) ?
- How about the coverage of every single C? 5X or 10x ? Is there a threshold ?
Another question about CpG methylation rates:
I have asked a question about how to define a CpG site. The answer seem to be that a CpG site is both cytosines in a CpG double strand site. Just like this:
forward strand: 5' ...CG... 3'
reverse strand: 3' ...GC... 5'
It's a CpG site. And here are read counts of it:
methylated counts of forward strand : 10
unmethylated counts of forward strand : 5
methylated counts of reverse strand : 8
unmethylated counts of reverse strand : 3
I think the methylation level of this CpG site is calculated as (10+8)/(10+5+8+3). Is this right?
Thank you very much for any comment.