How to Display Metadata on IGV Visualizations
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23 days ago
luminea ▴ 10

Hello everyone,

I am currently working with a .bed file containing genomic regions associated with different features: DMR (Differentially Methylated Regions), LMR (Low Methylated Regions), UMR (Unmethylated Regions), and histone mark peaks.

To simplify my analysis, I merged these different .bed files into a single .bed file to visualize all the regions on IGV . However, when I load this merged file into IGV, I lose the information about the specific type of region (DMR, LMR, UMR), or histone mark peak that I am viewing.

My question is ,is there a way to display metadata directly on the regions being visualized in IGV? Alternatively, could I add an extra column in my .bed file to annotate each region with its type (e.g., a "Type" column with values like "DMR," "LMR," "UMR," or "Histone_Peak") so that I can visualize and distinguish these features in IGV? Or is there another approach to achieve this?

Integrative-Genomics-Viewer IGV • 278 views
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Entering edit mode
23 days ago
GenoMax 149k

You can use color coding as described in:

https://groups.google.com/g/igv-help/c/gUvYp0imn9U
https://groups.google.com/g/igv-help/c/IyBzO5_j5E8

ItemRGB is described in BED format spec: https://genome.ucsc.edu/FAQ/FAQformat#format1

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