Call DMR using files in 10 bp bin format

[Greacy-x]

Hi yupeng,

I've obtained a batch of processed WGBS data from GEO database, which was generated using the 'methylpy allc-to-bigwig --bin-size 10' command, resulting in 10 bp bin format files (e.g., GSM4603053_allc_18.CGN.10bp.bw). I'm curious about how to utilize these files for DMR calling. Could you provide some guidance or suggestions on this matter?

Attached is an example of 10 bp bin format file.

Thank you in advance for your help!

[yupenghe]

You can use 10bp bin as a test unit. Converting the bigwig file to the allc format where each row corresponds to a 10bp bin will allow methylpy to perform differential methylation analysis.

[Greacy-x]

Thank you for your prompt response!

Meanwhile I'm considering comparing these public data with my own WGBS data, should I convert my own data into 10bp bin format and then use 10bp bin as a single unit for differential methylation analysis as you mentioned above?

Thank you once again for your time and expertise.

[yupenghe]

Yes I think that would be a valid strategy.

[Greacy-x]

Thanks a lot!