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CpG file for bismark mode -- mouse GRCm38 #2

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avilella opened this issue Oct 27, 2015 · 2 comments
Open

CpG file for bismark mode -- mouse GRCm38 #2

avilella opened this issue Oct 27, 2015 · 2 comments

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@avilella
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Hi, would it be possible to generate the input CpG file for mouse GRCm38 and make it available somewhere?

Alternatively, if there is a recipe for the creation of the bed file from the reference fasta file, can we make such recipe available somewhere?

Thanks in advance,

A.
@lidaof
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lidaof commented Oct 27, 2015

Hi @avilella , absolutely! Generating CpG file is very easy, we used the oligoMatch tool from UCSC kent source code. I could put the mouse file somewhere after I generated it.

@lidaof
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lidaof commented Nov 9, 2015

Sorry for late response. the mm10 files could be downloaded from https://cgs.wustl.edu/~dli/methylQA_Download/mm10/. thanks.

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@lidaof @avilella