bigWig Track Hub

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Jeff Long

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Aug 10, 2017, 2:20:06 PM8/10/17
to gen...@soe.ucsc.edu, bra...@soe.ucsc.edu

Hi Brian and Browser Group,

 

I have a track hub for bam’s and bai’s set up and working,

but for bigWigs data is not populating.

Do you see something that I am missing in my setup?

 

Best regards,

~Jeff

 

$ cat genomes.txt 

genome hg38

trackDb hg38/trackDb.txt

 

$ cat hub.txt 

hub DA0000011bw

shortLabel DA0000011bw

longLabel DA0000011 ChIP-Seq bigWigs

genomesFile genomes.txt

email jel...@celgene.com

 

$ cat hg38/trackDb.txt 

track lane5

bigDataUrl https://s3.amazonaws.com/celgene-bucket/[pathToMyData]/lane5_5.RemoveDuplicates-biobambam2.mdup.bw

shortLabel lane5

longLabel lane5 

type bigwig

 

 

Best Regards,

Jeffrey Long

Sr. Data Scientist

Celgene RIKU

1500 Owens Street, Suite 550

San Francisco, CA 94158-2332

(415) 515-8082

 

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Cath Tyner

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Aug 10, 2017, 5:54:46 PM8/10/17
to Jeff Long, gen...@soe.ucsc.edu
Hi Jeff,

Thank you for contacting the UCSC Genome Browser support team. 

As seen in example 4 of Step 7 on on the Track Hubs help page: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup
You will need to declare your data type as "bigWig" rather than "bigwig".

For a debugging tool, see the information about the command-line utility, "hubCheck" here:

In your trackDb.txt, try changing:

type bigwig

to

type bigWig

Also, I'm assuming that you're not literally using url https://s3.amazonaws.com/celgene-bucket/[pathToMyData]/lane5_5.RemoveDuplicates-biobambam2.mdup.bw, where the url is broken at "[pathToMyData]", which I believe you've used for security and just as a placeholder in your example. 

Please respond to this list if editing your trackDb.txt does not solve the issue so that we can provide further troubleshooting. 

Thank you for contacting the UCSC Genome Browser support team. 
​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

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​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute


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Jeff Long

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Aug 17, 2017, 12:35:06 PM8/17/17
to gen...@soe.ucsc.edu, bra...@soe.ucsc.edu

Any thoughts on this issue?

~Jeff

Cath Tyner

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Aug 17, 2017, 12:38:02 PM8/17/17
to Jeff Long, gen...@soe.ucsc.edu, bra...@soe.ucsc.edu
Hi Jeff, 

Thanks for checking in. I sent a response last week on August 10th to jel...@celgene.com. That response is included in this email thread, and I've also copied it again here, below. Please respond to this list if you have further questions!

Email from Aug 10th below:
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute


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Jeff Long

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Aug 17, 2017, 4:16:57 PM8/17/17
to Cath Tyner, gen...@soe.ucsc.edu, bra...@soe.ucsc.edu

Thanks Cath,

 

I found the email quarantined in the corporate spam filter. I’ve taught it to allow emails from you.

 

A trackDb.txt containing “type bigWig” does not display the data.

I think “bigwig” was an MS Outlook autocorrect; “bigwig” also throws an informative error message.

 

Yes, the [path to my data] bit was some obfuscation for the public email list.

Logged into the UCSC instance, a wget pulls the .bw so the permisssions seem OK.

Is there any chance the type bigWig does not recognize .bw?

Or is something else happening?

The process is working for bam/bai track hub, but not bigWigs.

 

Best regards,

~Jeff

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