custom track uploading problem

[Yecheng Huang]

Hi,

I use your Genome browser for my Dog assembly and annotation. This is a very great tool, thanks for the work.

When I tried to upload my own gtf file, I got this error:

needMem: trying to allocate 501484873 bytes (limit: 500000000)

The uploading file is about 800 MB, 120,000 transcripts. I take a subset ( 8000 transcript) to upload, it works.

Please advise any solutions.

Thanks a lot,

Yecheng Huang

EITS Georgia Advanced Computing Resource Center (GACRC)
University of Georgia

http://www.gacrc.uga.edu
706-542-9071

[Matthew Speir]

Hi Yecheng,

Thank you for your question about uploading custom tracks to the UCSC Genome Browser.

That file is far too large to loaded in a plain-text custom track format, such as GTF or BED.

Annotation files of this size should be converted into one of our compressed, binary formats, such as bigBed or bigGenePred. These formats are placed on a publicly-accessible web server and the URL to this location is supplied to the UCSC Genome Browser. The Genome Browser will then request the information it needs from the file as needed for only the regions of the genome you are currently viewing. You can read more about the bigBed format here: http://genome.ucsc.edu/goldenPath/help/bigBed.html, and more about the bigGenePred format here: http://genome.ucsc.edu/goldenPath/help/bigGenePred.html. Both of these pages describe the formats themselves as well as provide some information for converting your plain-text file into one of these formats using the command-line utilities we provide.

I should note that there is no "bigGTF" format and that you will need to convert your GTF file into either a BED or a genePred format before converting into one of the "big" formats. We provide the utilities gtfToGenePred and genePredToBed for converting your file between all of these different formats. You can find these two utilities and more on our downloads server here: http://hgdownload.soe.ucsc.edu/admin/exe/.

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

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[Yecheng Huang]

Matthew,

Thanks for the detailed response. My original gtf file is about 800MB. I am working on converting to bed then bigBed.

Another way is to trim the custom annotation to downsize the file size.

I will work this out and greatly appreciate your help.

Kind regards,

Yecheng Huang

EITS Georgia Advanced Computing Resource Center (GACRC)
University of Georgia

http://www.gacrc.uga.edu
706-542-9071

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From: Matthew Speir <msp...@soe.ucsc.edu>
Sent: Wednesday, April 13, 2016 11:52 AM
To: Yecheng Huang; gen...@soe.ucsc.edu
Subject: Re: [genome] custom track uploading problem