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isglobal-brge / methylclock

DNA methylation-based clocks
MIT License
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How to use MthylClock using Bed9+ file from WGBS as input #22

Open tawfikyoussef opened 2 years ago

tawfikyoussef commented 2 years ago

Hello,

I have Bed9+ files for WGBS and I wanted to estimate their ages. In the Bed9+ files, I have the beta values (in percentages) and the genome position rather than the CpG ID. Is there a way I could use this Bed9+ file directly, or use a tool/R Function to transform it to an accepted input format?

Thank you in advance!

faulk-lab commented 1 year ago

I'm commenting here in the hopes the authors have a solution to this question. Despite it being 1 year old, this is a problem of growing interest given the explosion of WGBS and Nanopore data.

Do the authors know of a way to convert chromosomal positions into cg##### annotation used by Illumina? That's the only step hindering the use of WGBS/WGMS with MethylClock. Would be great to have a solution!