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PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
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the question about hap1 and hap2 #57

Closed crazysummerW closed 1 year ago

crazysummerW commented 1 year ago

Hello! Thank you very much for developing such excellent analysis software. I have obtained the CpG analysis results of hap1 and hap2 (WGS). Now I want to analyze the DMR (Differentially Methylated Region) between hap1 and hap2. The amount of WGS data is too large for me to visually identify candidate regions effectively. However, I have not found any suitable software for PacBio data. Most of them are applicable to BS-Seq data. Could you please recommend any appropriate tools or analysis methods?

Looking forward to your reply. Thanks.

ctsa commented 1 year ago

Thanks @crazysummerW ,

@holtjma has recently released a tool, MethBat, which may help. It can process pb-CpG-tools output to classify the state of CpG Islands and identify anomalous methylation states relative to a background cohort. You can find more details here:

https://github.com/PacificBiosciences/MethBat

ctsa commented 1 year ago

Closing as answered.