Question: Question about details of the calculation of bisulfite conversion rates.
gravatar for hxlei613
3.5 years ago by
hxlei61390 wrote:

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.

ADD COMMENTlink modified 3.5 years ago by Devon Ryan97k • written 3.5 years ago by hxlei61390
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:
  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%.
ADD COMMENTlink written 3.5 years ago by Devon Ryan97k
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