WGBS data presentation

Question

[sinha.puja]

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.

[Papyrus]

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

Answer 1

[debora.gisch]

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,

Answer 2

[Binte.farooq]

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.