bedGraph Track Rendering Issue

[Alain Pacis]

Dear UCSC Genome Browser Team,

I would like to report a potential rendering issue with bedGraph tracks in the UCSC Genome Browser.

Link: https://genome.ucsc.edu/s/apacis/Naoumova_WGBS_mouse_brain

When viewing certain genomic regions (for example, chr12:35,396,245-35,397,089), two of my bedGraph tracks (XX Methylation and XO Methylation) appear as a solid filled block rather than individual bars. Other regions of the genome render correctly for these same tracks, and the other tracks created using the identical script render correctly throughout the genome.

Details:

- Track type: bedGraph

- Data: CpG methylation values (range 0-1)

- Track header: visibility=full, autoScale=on, windowingFunction=mean

- Genome assembly: mm10

- Affected tracks: XX Methylation, XO Methylation

- Example region with issue among others: chr12:35,396,245-35,397,089

- Observed behavior: solid filled block

- Expected behavior: individual bars with visible gaps between data points

Since all tracks were generated with the same script and the issue is region- and track-specific, this suggests a rendering issue rather than a data formatting problem.

Thank you for your time and for maintaining such an invaluable resource.

Alain Pacis, PhD
Bioinformatics Specialist
Canadian Centre for Computational Genomics
Rosalind and Morris Goodman Cancer Institute

https://computationalgenomics.ca/services/

[Matthew Speir]

Hello, Alain.

Thank you for your question about visualizing bedGraph data in the UCSC Genome Browser.

Can you share the bedGraph files that you're having issues with? This should help us debug further so that we can understand the difference between the underlying data and visualization.

You can send these files to our private mailing list at genom...@soe.ucsc.edu, which is accessible only to UCSC Genome Browser staff.

Thank you!

---

Matthew Speir

UCSC Genome Browser, User Support

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