trackViewer: File format detection
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@tomasrodriguez-21656
Last seen 7 months ago

Hi Jianhong and Julie,

When using browseTracks, I am unable to use some files once mounted if their extensions don't exactly match known strings. The following messages appears when importing bigwigs with ".bw" extensions, for example:

Can not detect the format of the file. Please rename the file with end of .BED, .bedGraph, .WIG or .BigWig

Is there a way to expand the library of recognizable extensions or assign an alias? Once mounted, it's very cumbersome to unmount, change extensions, remount and reload the relatively bulky dependencies like TxDb, org etc.

Thanks for the help!

Tomás

trackViewer trackview • 180 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 21 days ago
United States

Hi Tomas,

Thank you for trying trackViewer. I suppose you are using function importData to import the '.bw'. Did you tried to set the format argument to 'BigWig'? Let me know if you still have any question.

Jianhong.

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Hi Jianhong,

I am trying to use the BrowseTracks function. Unfortunately, the importData function freezes inside the docker container after ~5min of trying to import my bigwigs, even with 24G of memory allocated to the container. No error has populated, so I'm not sure what the issue is.

Tomás

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Hi Tomas,

Did you tried to assign gr parameter? This parameter is used to limit the imported data region. Otherwise it will read all data into memory. Please try to read the help documentation by ?browseTracks for more details.

Jianhong.

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