problem with uploading track file

[Muthu, Victor]

Dear UCSC browser support,

First of all, thanks for hosting the browser. It's been an invaluable tool for me and the general scientific community.

I'm trying to upload a large chip-seq track file (bedgraph) and was asked to convert to bigwig by the browser. I did that and when I tried uploading the bw file, this error message appeared:

Error File 'Chip_seq_sam1.ucsc.bw' - It appears that you are directly uploading binary data of type bigWig. Custom tracks of this type require the files to be accessible by public http/https/ftp, and file URLs must be passed as the bigDataUrl setting on a "track" line. See bigWig custom track documentation for more information and examples. 

I don't really understand what it means but I guess that it wants me to share the file publicly prior to uploading it onto the browser? My data is yet to be published and I do not want it to be publicly accessible for now. Is there another way for me to upload my data onto the browser?

Appreciate your help.

Thanks,

Victor

p.s. I've never experienced this problem before. My guess it's probably due to the large file size (712MB for bw and 4 GB for bedgraph)

[Cath Tyner]

Hello Victor,

Thanks for contacting the UCSC Genome Browser support team. 

Here are some helpful resources for getting started with custom tracks:

http://genome.ucsc.edu/goldenPath/help/customTrack.html#MANAGE_CT

Specifically, here is a bigWig example with step-by-step instructions for loading a bigWig custom track:

http://genome.ucsc.edu/goldenPath/help/bigWig.html

Yes, you are correct; note in 'Step 6' that you'll need to move the file into a web-accessible http, https, or ftp location. That location must also allow byte-range requests, meaning binary files like BAMs, bigBeds and bigWigs can be hosted there.

Our software does not require completely open access to your data files via FTP or HTTP; we also support HTTPS connections. To set up files for remote access as a custom track or track hub, the faculty member would have to include the HTTPS credentials needed to access the files. See more information here:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/cUpkev4xrGo/ZHdK-09gFBcJ

You might be interested in hosting your data on CyVerse, a free NFS funded site created for assisting data scientists with data storage needs.

Using CyVerse with the UCSC Genome Browser:

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting

You can also ask CyVerse more about privacy and access control:

http://www.cyverse.org/security-and-privacy-policy

http://www.cyverse.org/get-help

One option for complete privacy is more time-intensive, but it is an option -

Setting up a mirror installation with Genome Browser in a Box:

http://genome.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/

http://genome.ucsc.edu/goldenPath/help/gbib.html

http://genome.ucsc.edu/goldenPath/help/mirror.html

Thank you for contacting the UCSC Genome Browser support team. 

​

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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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