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Nik-Zainal-Group / MMRDetect

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hg38 support #1

Open pdiakumis opened 2 years ago

pdiakumis commented 2 years ago

Dear @xqzou, Thanks for this very promising tool. I was wondering if hg38 can be supported for MMRDetect? The paper mentions that you used hg19 for all analyses, and I can see hg19-specific code snippets in Gen_catalogues.R.

Kind regards, Peter

xqzou commented 2 years ago

Dear Peter,

Thank you for your interest in MMRDetect. I agree with you that hg38

should be supported for MMRDetect. However, I have left the Nik-Zainal group, so I am not in a position to make changes to the MMRDetect anymore.

Sorry for not being more helpful.

Best wishes,

Xueqing

On Sun, Feb 6, 2022 at 12:59 PM Peter Diakumis @.***> wrote:

Dear @xqzou https://github.com/xqzou, Thanks for this very promising tool. I was wondering if hg38 can be supported for MMRDetect? The paper mentions that you used hg19 for all analyses, and I can see hg19-specific code snippets in Gen_catalogues.R https://github.com/Nik-Zainal-Group/MMRDetect/blob/master/R/Gen_catalogues.R .

Kind regards, Peter

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DarioS commented 1 year ago

Any progress of finding a new maintainer and getting this done? I also have sequencing data in reference to hg38. I suppose that I could just do a mutational signatures analysis and check for non-zero SBS6 proportion.