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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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A question about the frequency threshold determination #44

Closed Wyinghao closed 1 year ago

Wyinghao commented 1 year ago

I used the call_freqb as described and output the BED file, column 11 of the file is the frequency and likelihood of methylation sites, I would like to ask you if there is a recommended filter value (how much frequency should be greater) as a trusted methylation site.

PengNi commented 1 year ago

Hi @Wyinghao , thanks for using our tool. In my opinion, there's no common thresholds for methylated or unmethylated sites. It depends on the problem and the data. Generally, I would take >=0.7, <=0.3 to get highly methylated and lowly methylated sites, respectively.

Best, Peng

Wyinghao commented 1 year ago

Hi，peng！Thank you very much for your reply，I will adopt this standard that you recommend！

PengNi commented 1 year ago

Closing this issue as it is inactive. If further issues arise, feel free to reopen this issue.