pmd output (5th column)

[Juheon Maeng]

Hi all,

I am using methpipe-3.4.3 to call PMD using "Human_BCell-chr19.meth" as an input. I used the command "pmd -b 100 -i 15 -o Human_BCell-chr19_newformat.100.pmd Human_BCell-chr19.meth".

PMD output is like 

chr19 217596 218742 PMD0 11 +
chr19 241093 242851 PMD1 19 +
chr19 245041 246418 PMD2 13 +
chr19 294726 296229 PMD3 15 +
chr19 332397 333894 PMD4 13 +

I thought the 5th column is the number of CpGs in each PMD as I looked the code in the github.  (https://github.com/smithlabcode/methpipe/blob/2f55e5f0e953fc28d93776afdc5b0819da7ff99d/src/analysis/pmd.cpp)

However, when I manually count the number of CpGs in the input for the first PMD (PMD0), there are 91 CpGs in the input file not 11 as indicated in PMD output.

Is the 5th column not the number of CpGs? 

Best regards, 
Ju Heon Maeng

[Ben Decato]

Hi Ju Heon,

Thanks for using methpipe. Sorry for the typo -- the fifth column in the PMD program's output is actually the number of bins in the PMD. Also, I would suggest not using a bin size lower than 1kb to identify PMDs, to prevent misidentifying hypomethylated gene promoters and enhancers as partially methylated domains, which are typically in the hundreds of kilobase to megabase scale. 

Ben

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Benjamin Decato, Ph.D.
Computational Biology Section,
Department of Biological Sciences,
University of Southern California
1050 Childs Way, RRI 408M
Los Angeles, CA 90089-2910

[Juheon Maeng]

Thank you for the clarification!

Best regards,
Ju Heon Maeng

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