Similar bed files not showing data in whole genome view

[Adam Clayton]

Long time user of IGV, but I'm seeing a behavior I can't explain. I'm using hg19 and the latest version of IGV 2.17.4. When I drop the attached bed files into IGV, in the whole genome view, I can see blue vertical bars indicating the location of annotations in the file beginning with "MYECNV_", but in the file beginning with "MYE_", I don't see any blue vertical bars. I can zoom into chromosomes containing annotations and see them in both files, but not on whole genome view. Both headers are identical in the files and annotations are formatted consistently in both files. Please let me know if there's something I can do to get IGV to display the annotations in the whole genome view for the MYE_ file.

Thank you,

-Adam

[igv-help]

Hi Adam,

Yes that is strange. We'll look into it.

Helga

[igv-help]

Hi Adam,

We found the issue and the fix will be included in the next IGV release.

We don't have an estimated release date yet, but in the meantime the fix is in the IGV development snapshot build, which you can download from here.

Helga

[igv-help]

One more thing to note. The issue has to do with files that have no entries for chromosomes 1 or 2. 

For your file that doesn't work, if you add a dummy entry say on chromosome 1 from bp 0 to 1, the file will correctly display the whole genome view even in versions of IGV that still have the bug.

So that would be a workaround if you prefer not to use the development snapshot version.

Helga

[Adam Clayton]

Thank you for identifying the cause of this bug. 

Can you let me know when the fix has been added to a full release (and the version number) so that I proceed with testing to confirm functionality.

-Adam

[igv-help]

Hi Adam,

Yes - we will try to let you know as soon as it is released. But have you tried the development snapshot version to confirm it works for you?

Helga

[Adam Clayton]

Yes, I’ve confirming things are working in the latest snapshot build. Thanks for following up. 

-Adam

On Apr 18, 2024, at 10:23, igv-help <igv-...@googlegroups.com> wrote:

Hi Adam,

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/4DwunTfWDD0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/317258c6-6a99-4982-841c-8d8f1e86cd3an%40googlegroups.com.