Visualize methylation status in Pacbio Hifi read

Question

[Cathy]

I want to know how to visualize methylation status in IGV. I tried to visualize by clicking color alignments by -> base modification (or bisulfite mode -> CG). But It shows only red colors and no blue colors in IGV.

Please let me know how I can solve this problem.

Answer 1

[Billy Rowell]

Before trying anything more complicated, make sure you're using the most recent stable release of IGV, v2.16.1.

[Cathy]

I didn't realized the version problem. I update the version of IGV and it works. Thanks a lot.

Answer 2

[Chris Saunders]

With a newer version of IGV, the option you need to display 5mC that adds blue for hypomethylated sites is:

"Color alignments by" -> "base modification (5mC)"

More detail provided here:

https://github.com/igvteam/igv/wiki/5mC-coloring-mode

[Cathy]

Thank you for your detailed explanation.

Answer 3

[andorjkiss]

This seems to have issues (errors and crashes) with the lasted output data by REVIO and VEGA; however JBrowse seems to work.

[cmdcolin]

(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with modifications but it is a very complex specification. the igv devs are also pretty responsive so if you report the bug to them they may be able to fix it on their end too