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WGBS data presentation

Hi All,

I have the data from WGBS where I have the input format which includes columns of Chr, start position, end position, average methylation values. I wanted to show the global methylation patterns using plot as shown in the reference figure.

Please help me in providing the suggestions for making such plot.

Thanks in advance.

Figure reference for plot

wgbs r

Maybe you can use the Gviz R package (see section 4.3).

2 answers

Your question is not clear for me. If the file extension is a bedgraph file you can plot and see tracks throughout the genome with tool called IGV. (Do you need to know the genome reference hg19 or hg38) If your files aren't a bedgraph files you can build a file with information do you have. See the bedgraph file format USCS https://genome.ucsc.edu/goldenPath/help/bedgraph.html I hope this help you,

HMST-Seq-Analyzer (https://hmst-seq.github.io/hmst/) outputs some graphs for global methylation patterns. may be look into the paper for some ideas about figures you can get with that tool.

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