bigWig track in GBiB

Alegre, Gimena

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Dec 2, 2020, 12:06:09 PM12/2/20

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Hello,

I’m trying to learn how to upload a bigWig custom track to my GBiB. Is there a way to create this bigwig track directly into GBiB using the path to the file (without using the BigDataURL)? For example, if I use a track line format like this one: track type=bigWig name="Example One" description="A bigWig file" color=255,255,255 /home/mydatafolder/Example1.bw. Is it required that I share my folder (“mydatafolder” in this example) through my VirtualBox first?

Thank you for the help!

Best Regards,

Gimena Alegre

Research Associate

Department of Neurobiology

University of Massachusetts Medical School

Jairo Navarro Gonzalez

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Dec 3, 2020, 1:04:20 PM12/3/20

to Alegre, Gimena, gen...@soe.ucsc.edu

Hello Gimena,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The following GBiB help page about loading local files should be able to answer your questions:

https://genome.ucsc.edu/goldenPath/help/gbib.html#LocalTracks

Once you have the directory with your file shared through VirtualBox, i.e. /home/mydatafolder,
you can then load the track by using the following track line attribute:

bigDataUrl="http://127.0.0.1:1234/home/mydatafolder/Example1.bw"

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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Alegre, Gimena

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Dec 3, 2020, 1:29:54 PM12/3/20

to Jairo Navarro Gonzalez, gen...@soe.ucsc.edu

Thank you. I saw that GBiB help page before, I just wanted to see if there was another option for uploading my bigwig file. Perhaps just uploading the bigwig file using the “Browse…” button above the data text box? But maybe that option is not available for bigwig format.

I appreciate your help!

Best Regards,

Gimena Alegre

Research Associate

Department of Neurobiology

University of Massachusetts Medical School

Lazare Medical Research Building, Room 760B

364 Plantation Street, Worcester, MA 01605

Phone: (508)856-4415

Daniel Schmelter

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Dec 3, 2020, 2:42:19 PM12/3/20

to Alegre, Gimena, Jairo Navarro Gonzalez, gen...@soe.ucsc.edu

Hello Gimena,

We don't currently have any option to upload big* files directly with the upload button. As we mentioned, the method for uploading big* files is to reference them with the local path. I have made a note of your suggestion and we will consider it for future development. Thank you for writing in and for your suggestion.

If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

Daniel Schmelter
UCSC Genome Browser

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/7BCCB352-F7CB-4F09-B442-80FF1B440C5F%40umassmed.edu.

Alegre, Gimena

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Dec 3, 2020, 3:15:55 PM12/3/20

to Daniel Schmelter, Jairo Navarro Gonzalez, gen...@soe.ucsc.edu

Thank you for the information!

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