IGV track display problem: interval rectangle from BED file appears above all tracks in white, overlapping each other
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10 days ago
mcsimenc ▴ 30

If I load a BED file, it shows the interval rectangles above all other tracks, and if I have multiple loaded and the same interval is in each, the rectangles overlap each other, all at the top, no matter how I rearrange the tracks. The feature name appears where expected, wherever the track is in the list and at that position.

This happened suddenly, I think after updating my system (Manjaro). I installed the latest version of IGV from the Arch User Repository, but it still has the same problem. I was thinking maybe it's a problem with the Java version being used.

Has anyone seen this and have insight into what is causing it, and how to revert it to the usual behavior where features appear with their tracks?

Note: I also tried searching for the feature name in the box, e.g. Chr1-154, but it didn't bring anything up. Maybe because the names are prefixed by the chromosome name, or related to the display problem?

White box at top

IGV bed • 1.5k views
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Entering edit mode
10 days ago
mcsimenc ▴ 30

The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.

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