questions about the assembly hub

[吴薇]

Dear Sir,

I made an assembly hub for a new reference genome and then when I try to make an annotation bigbed file as a track, I found only black boxes are shown and one example is attached. I wonder how I should modify my bed file or configure my track information to let the label shown next to the box like a normal track we usually find UCSC genome browser. For example, the RefSeq annotation in hg19. I tried some display settings, but failed to find the correct one.

Look forward to your reply!

Thanks!

Wei

[Matthew Speir]

Hello, Wei.

Thank you for your question about the display of assembly hub tracks in the UCSC Genome Browser.

It's likely that you just need to properly declare the track type in the trackDb statement for this track. For example, if you have a 12 column bigBed file, then the type line in trackDb should read:

type bigBed 12

The number after "bigBed" should match the number of columns in your file.

If you are looking to display genes on your assembly hub, you should look into the bigGenePred format, which has some display features designed specifically for gene predictions. You can read more about bigGenePred here: http://genome.ucsc.edu/goldenPath/help/bigGenePred.html.

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.

Matthew Speir

UCSC Genome Bioinformatics Group

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

Outreach, User Experience, Quality Assurance and User Support

HCA, CIRM, and UCSC Genome Browser

UCSC Genomics Institute

[吴薇]

Hi Mattew,

Thank you so much for your quick reply! I just fixed this problem and I made it searchable by the gene symbol. However, it is case sensitive, so I wonder is there a way to make it not case sensitive?

Thanks again!

Best,

Wei

[Matthew Speir]

Hello, Wei.

I apologize for taking so long to respond.

You will need to combine the search index you have already created with another search index called "trix". Here are some helpful links about making tracks in your hub searchable:

• Basic information about search trix files and an example hub can be found here: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Search. 
• Information about using the searchTrix setting in your trackDb: https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#searchTrix
  
• Instructions for building a search trix file: https://genome.ucsc.edu/goldenPath/help/trix.html

More info can be found in the following answers to previous mailing list questions:

• https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/sXu4x679eQ4/8RTLqGcqFwAJ
  
• https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/1dG6Wi1htFk/k2HoOmNhGokJ 
  

I hope this is helpful. If you have any further questions, please reply to genome...@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.