Zebrafish table browser Expression and Regulation track issue

[Rachel Dveirin]

I wasn't sure if I should start a new conversation or reply somewhere in the "Error in loading Danio code track hubs to UCSC" conversation, but I have a question/issue I think might be related? I'm trying to download the annotation files for zebrafish expression and regulation files from the table browser (assembly GRCz11/danRer11), but it wont let me select the "JASPAR Transcription Factors" option. 

Thank you!

[Brian Lee]

Dear Rachel,

When the JASPAR track is selected this note displays on the Table Browser: 

Note: This track is unavailable for genome-wide download. Reason: JASPAR files contain billions of items. The Table Browser allows regional queries for this track, but those may timeout if the regions are too big. See the Data Access section in the track description page for other ways to query this data, such as command-line tools and our API.

An alternative approach to access the data is to display the JASPAR track in the region of interest on the Browser and go to the "Downloads" top menu bar, and select "Download Current Track Data" to obtain a JSON snapshot of the displayed data. 

All the best,

Brian Lee

[Gerardo Perez]

Hello, Rachel.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

As Brian mentioned, due to the size of the JASPAR dataset, the Table Browser does not allow “Genome” as a query region for the JASPAR track, but it does support regional queries, which may time out over large regions.

The Data Access section of the JASPAR track description page provides additional ways to obtain the data. As Brian noted, one option is the Download Current Track Data feature available from the “Downloads” blue bar menu.

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.

Gerardo Perez
UCSC Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/9d45923a-f511-4062-88ef-6ca177604305n%40soe.ucsc.edu.

[Rachel Dveirin]

thank you! That was very helpful. I had one other question regarding zebrafish annotation availability, for the DANIO-CODE annotation track:
Missing required setting 'hub' from https://danio-code.zfin.org/trackhub/DANIO-CODE.hub.txt    

When I hovered over the info for the error - it said to "Contact us or the hub provider if you cannot resolve the issue." Could you possibly help with this as well?

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The URL being loaded on the UCSC Genome Browser is not the actual hub.txt file needed to view the track hub. Unfortunately, it appears the DANIO-CODE website is serving the wrong file via its URLs, so please contact them to resolve the issue. When you contact them, please CC us so we can provide additional information about the problem if needed.

dani...@gmail.com

To view the hub, please use the following URL:

https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt

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.

Jairo Navarro
UCSC Genome Browser

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOh4Tc-WLfS-Jo2YGr1W4CvKY%3DHrabuKpVN%2BPaNhLZzfvmTETQ%40mail.gmail.com.