Question about details of the calculation of bisulfite conversion rates.

Question

[hxlei613]

Hi! I wonder some details about the calculation of bisulfite conversion rates.

1. It seems that conversion rate can be calculated using all types of C ( CpG, CHH, CHG ) ?
2. How about the coverage of every single C? 5X or 10x ? Is there a threshold ?

Another question about CpG methylation rates:

1. 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.

Answer 1

[Devon Ryan]

1. It's generally preferable to use only CHH and/or CHG sites for calculating the conversion efficiency? The reason is that CpGs often be methylated, while the other contexts won't be and this non-CpG methylation level is often constant across biological treatment groups. So, the conversion rate is then simply 1-%"apparently methylated Cs in a non-CpG context".
2. You don't need a threshold for use in conversion efficiency.
3. Yes, the methylation level is 18/26, or ~70%.