CpG Density with respect to TSS
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3.4 years ago
ResearchR ▴ 90

Dear all,

I would like to replicate an analysis from the paper "Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing". In more detail, I try to reproduce the plot 1a. Does anyone of you know, how this plot has been created. I am struggling to calculate the density of CpGs with respect to the TSS location. It seems to that this is actually a density plot, with two dimensions.

Help is very well appreciated!

Chris

R Methylation density sequencing ngs • 1.2k views
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Reads to me link like a simple percentage of CpGs per total nucleotides in a certain bin. What I would probably do is to take the center position of all your TSS in bed format. From this go 20kb in each direction, and then subdivide this 40kb windows into bins of, say, 100bp. This all can be done with bedtools makewindows. Once you have this, simply count the number of CpGs per bin, and then divide this number by 100 to get the density. This is just a technical solution. Which regions you then take depends on the question that you want to answer.

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Thanks for the suggestion! I will give it a try!