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guoweilong / cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
https://cgmaptools.github.io
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cgmapstat #47

Open zhangaicen opened 3 years ago

zhangaicen commented 3 years ago

Hi Guo, sorry to disturb you again, but I still have some questions. I used cgmapstat to obtain relative information with the rice.CGmap.gz as input. The result is as the picture show: cgmap In the plant genome, we always pay attention to CG, CHH, CHG, and in the column 4 of CGmap.gz, it also only have three classes of DNA methylation, so how the CA, CT, CC, CW..... in the *.mstat.log come? They are not belong to CHH or CHG?

I used zcat CGmap.gz| awk '$4=="CG"' >CG.txt to count the CG (CHG, CHH)methylation sites, but if in the CG.map.gz there are also CA, CT... how could I get the accurate CG ,CHG and CHH sites?

Thank you for your patient reply. Zhang

guoweilong commented 3 years ago

The column 5 of CGmap file is defined as nucleotide pattern. For example, CA, CC, CG, CT. And CGmapTools will utilized this column for identify a nucleotide context.

Weilong

At 2021-02-24 16:41:57, "zhangaicen" notifications@github.com wrote:

Hi Guo, sorry to disturb you again, but I still have some questions. I used cgmapstat to obtain relative information with the rice.CGmap.gz as input. The result is as the picture show:

In the plant genome, we always pay attention to CG, CHH, CHG, and in the column 4 of CGmap.gz, it also only have three classes of DNA methylation, so how the CA, CT, CC, CW..... in the *.mstat.log come? They are not belong to CHH or CHG?

I used zcat CGmap.gz| awk '$4=="CG"' >CG.txt to count the CG (CHG, CHH)methylation sites, but if in the CG.map.gz there are also CA, CT... how could I get the accurate CG ,CHG and CHH sites?

Thank you for your patient reply. Zhang

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zhangaicen commented 3 years ago

I know that colume 5 will show the pattern , but if in colume it is "CT", how to define it is "CHH" or "CT"?

guoweilong commented 3 years ago

CGmapTools uses both columns for counting. For example, CTT is CHH type and also is CT type.

Weilong

At 2021-02-24 16:51:42, "zhangaicen" notifications@github.com wrote:

I know that colume 5 will show the pattern , but if in colume it is "CT", how to define it is "CHH" or "CT"?

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zhangaicen commented 3 years ago

Thanks , I've got id, thanks very much for you patience.