bigBed file behaves differently in a hub than as a custom_track??? no gene names!

[Hendrickson, Curtis (Campus)]

Dear TrackHub folks

Here’s a session and a hub for the question below:

https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Curtish&hgS_otherUserSessionName=SR_test_hub_SR10%2D01

https://data.genome.uab.edu/ccts/bmi/ics/ross,s/track_hub/

It contains the de novo contigs from a viral genome sequence, some gene annotations (bed/bigBed) and a set of mapped reads (bam).

I have a problem with the bigBed display, and  a question about configuring default BAM file display.

We created some bigBed files that show gene annotations mapped from similar strains via Exonerate.

When I load these as “custom_tracks” and view them in “full” mode, they nicely display their gene names (column 4 of bed file)

However, when I use the same .bb file inside by track_hub, to comes up grey, with no names at all, and the introns are not displayed, all of which is quite dismaying. I figure I’ve messed up some configurations in the trackDb.txt file, but haven’t been able to figure out what I’ve done wrong.

 

Hub/BigBed problem screen shot:

BAM file question:

In this session I’ve set the bamfile as a bargraph, but I can’t figure out how to specify in trackDb.txt that it should default to that display mode. I don’t see any tags for that at https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

 

Regards,

Curtis

 

PS _ thanks again for your great help in the past!

[Cath Tyner]

Hi Curtis!

Here a few suggestions, below. Please respond to this forum if the suggestions below do not solve the issues you're having with your hub - our support team would be happy to help troubleshoot further if needed. 

* Specify the bigBed type, e.g. "bigBed 4" or "bigBed 6".

* You might need bigBed 12 + to get the introns as well (this should resolve the color issue also). 

* You may also want to swap useScore 1 for spectrum:

From trackDb.txt

​:​

longLabel All Virus Genes
useScore 1
type bigBed

Please respond to this list if you have further questions!

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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