UCSC session track using BigWig files on Zenodo

[Francesco Gandolfi]

Dear UCSC team,

I am writing to you for assistance regarding an issue with accessing BigWig files, currently deposited on Zenodo under restricted access, within the UCSC Genome Browser.

We need to share a UCSC session of these BigWig files with external reviewers for a manuscript currently under peer-review. The challenge we are facing is that, due to the restricted access settings on Zenodo, the UCSC Genome Browser is unable to retrieve and visualize these BigWig files. Consequently, the shared UCSC session appears as shown at the following link. 

The point is that we would need to maintain the Zenodo record under restricted access until the associated manuscript is officially published. Unfortunately, my current understanding is that the only way to successfully visualize the UCSC session is to set the Zenodo record to 'public/open' status.

Could you please advise if there is any solution or alternative workflow that would allow reviewers to access our BigWig files via a UCSC session while the Zenodo record remains under restricted access? 

Thanks a lot for the help.

Best regards

Francesco

[Matthew Speir]

Hello, Francesco.

Thank you for your question about loading custom tracks in the UCSC Genome Browser.

Unfortunately, Zenodo does not create URLs that are usable with the way the UCSC Genome Browser requests data. You will need to find another hosting service. We do list some alternatives here: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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[Francesco Gandolfi]

Dear Matthew,

First of all, thanks a lot for the kind response and the help. 

Just for clarification, in our case the Zenodo URLs used for the UCSC tracks actually work on the GenomeBrowser and I can visualize them correctly if the Zenodo record of BigWigs are deposited on the 'open/public' status. The issue arises only when I put the Zenodo record under restricted access (making data accessible only with link, sharing etc...). In that case, UCSC browser cannot reach the zenodo URLs and tracks are removed from visualisation (as you could see in the link).

In light of this specific behavior with Zenodo's restricted access, could you please confirm if using one of your suggested alternative hosting services, such as Figshare, would resolve this issue? For example, if BigWig files are deposited in a Figshare item under restricted access (e.g., shared only via private link or reviewer token), will they be successfully visualized on a UCSC session, even with Figshare's restricted access settings activated?

Thank you again for the support and suggestions.

Kindest regards

Francesco

[Clay Fischer]

Dear Francesco,

One of our engineers shared that Zenodo's restricted access requires OAuth, so it will not work with our servers. It is quite likely that similar restricted access data hosting also uses OAuth. 

Instead, we recommend using Hub Space as described in a previous email.

Thanks,
Clay Fischer
UCSC Genomics Institute

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/15969318-82d5-4bb3-947a-3bdea0b29807n%40soe.ucsc.edu.