Methylation Data: Igv?
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Entering edit mode
10.3 years ago
Rm 8.2k

I have methylation data :

 chr coordinate methylation_score
    1     1203457 0.5
    2      1307889 0.9 
....

How do I plot them in IGV. I want it to display as bar or heatmap according to the methylation score. I converted above data to .bed file; I can visualize, but not according to the scale of methylation score.

Does the data need to be any other format?

Thanks for your inputs.

igv methylation file format • 5.3k views
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2
Entering edit mode
10.3 years ago
Rm 8.2k

After going through IGV manual little deep; Icould able to plot it. SEG file format could support the methylation data to report it as heatmap or bar graphs. I plotted "methylation read coverage" as "num.mark" and methylation_score (C/C+T) as "seg.mean" Example: example.seg

ID      chrom   loc.start       loc.end num.mark        seg.mean
#type=DNA_METHYLATION
Sample_1  1       566715  566715  53      0.0377358
Sample_1  1       566740  566740  54      0.037037
Sample_2  1       566732  566732  50      0.02
Sample_2  1       566724  566724  55      0.127273
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