Table Browser - Gene Hancer

[Rina Ben-El]

Hi, 
How are you?
I am unable to output the files to a readable format. 

The first attachment is what I have selected, and the output attached is what I receive, I have also saved the output as a pdf as I can see it in my web browser. 

Can you please advise. 

Thanks 

[Jairo Navarro Gonzalez]

Hello,

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

Can you explain what you mean by "readable format"? Do you wish to have a file that can be viewed on a spreadsheet?

In the subject line of your email, you mention the GeneHancer track but the screenshot shows the Table Browser using the GENCODE V41 track for hg38. You will have to select the GeneHancer track to get data for that track. If you want to save the Table Browser output to a file, you can add a file name to the "output filename:" field.

If you are new to using the UCSC Genome Browser, you may find the following training page helpful. There is a YouTube video tutorial about how to determine which table belongs to a track. There is also a Table Browser User Guide available for advanced queries:

Training page
Which tables belong to a data track
Table Browser User Guide

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

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[Rina Ben-El]

Hi Jario, 

My goal is to get the list of genes between two genes, which I learnt from this tutorial (https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#listOfGenes) is done by using the Table Summary method. 

Thank you for clarifying the output filename, it now works as it should. 

Last, is the hgTable not coming from the Gene Hancer predictions themselves?

Rina 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your follow-up question.

We imported the predictions from GeneHancer, which was last updated in 2019. However, the Table Browser does not output the GeneHancer predictions for the entire genome. This is due to our agreement with the Weizmann Institute and you learn more from the Data Access section on the GeneHancer description page (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr19&g=geneHancer):

Due to our agreement with the Weizmann Institute, we cannot allow full genome queries from the Table Browser or share download files. You can still access data for individual chromosomes or positional data from the Table Browser.

GeneHancer is the property of the Weizmann Institute of Science and is not available for download or mirroring by any third party without permission. Please contact the Weizmann Institute directly for data inquiries.

You can request the data using the following URL:

https://www.weizmann.ac.il/pages/contact

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