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Windows IGV Desktop v2.19.1 Doesn't Recognize Interact-Format .bed Files #1637

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NikoBlank opened this issue Jan 8, 2025 · 2 comments
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@NikoBlank
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Issue in the title; loading the interact example file with the IGV webapp works as expected:

An interact track with arcs sprouting from chromosome 3

Loading the same file with the IGV desktop app on Windows initially displays a track that seems to be displaying feature concentration:

A track with a single blue peak on chromosome 3

that, upon zooming in, seems to just display some amount of feature coverage (shown here in squished view; collapsed view displays a single row of blue representing the union of all features):

A track with multiple blue bars scattered within a region

I've double-checked with an interact file of my own that this is not unique to the example file; my file similarly rendered as expected on the webapp, but not the desktop app.

@jrobinso
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jrobinso commented Jan 9, 2025

Yes I mis-spoke earlier, desktop will treat interact (and bigInteract) files as generic bed files. I'll treat this as a request, but can't give an ETA at the moment. For desktop I suggest you stick with bedpe for now.

@NikoBlank
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Fair 'nough.

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