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Methylation calling question #1

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PanZiwei opened this issue Jun 10, 2020 · 0 comments
Open

Methylation calling question #1

PanZiwei opened this issue Jun 10, 2020 · 0 comments

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@PanZiwei
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Hi,

I have some questions about your quantify methods on 5mC/5C and would really appreciate it if you can help!

  1. You mentioned that "CpG sites with a methylation level higher than 3% in bisulfite sequencing were designated as methylated", why do you choose 3% as a cut-off? Any experimental/theoretical evidence? So the 3% is for several CpG sites in a region, or for one CpG site?

  2. For a specific CpG site, are you only calling two states: methylated/unmethylated? Or you calculate the 5mC% at the specific CpG site? Or calculate 5mC% in several CpG sites located in a region?

  3. In README file you mention the call methylation, Is it a percentage calculation? If so, what region do you calculate to get the percentage?

  4. Can lrTAPS call 5hmC or calculate 5hmC% at this stage?

Thank you so much for your help!
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