Missing output format option

Azeem, Muhammad

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Jun 2, 2025, 1:09:40 PM6/2/25

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Hi

I am trying to extract GRCh38/hg38 assembly using table browser. In the output section I need to put the output format “selected fields from primary and related tables” option. But when I click on the drop down menu, this option is not available, although in the help section I read this option should be available. So can you please explain why I cannot find this option? If there is a change to some alternative option available for extracting the similar information then please let me know.

Thank you.

Best regards,

Muhammad Azeem

============================

Dr. Muhammad Azeem

University Hospital Wuerzburg,

Medicine Clinic and Polyclinic-II,

Jundt's group –

Molecularly Targeted Therapies,

Versbacher Str. 5, House E4,

D-97078 Wuerzburg,

Germany.

Tel: +49 (931) 201-71030

Email: Aze...@ukw.de

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Luis Nassar

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Jun 2, 2025, 1:12:32 PM6/2/25

to Azeem, Muhammad, gen...@soe.ucsc.edu

Hello, Muhammad.

That option is not present on all data types. Could you share what data you are looking to extract and what specific fields you would like in the output?

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Lou Nassar
UCSC Genomics Institute

Azeem, Muhammad

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Jun 3, 2025, 2:59:47 PM6/3/25

to Luis Nassar, gen...@soe.ucsc.edu

Hello Luis

Thank you for your response. Please see the below screenshot for my selection of data. Additionally, I am interested in having information about transcription start and end, exon start and end, CDS region, chromosome, genes and strand information in the output. The said output format was working and the option “selected fields from primary and related tables” was available a few weeks ago and I have used it for the same Genome assembly as shown in the image. But now somehow it is not available anymore. Please let me know why it happend?

Thank you.

Best regards,

============================

Dr. Muhammad Azeem

University Hospital Wuerzburg,

Medicine Clinic and Polyclinic-II,

Jundt's group –

Molecularly Targeted Therapies,

Versbacher Str. 5, House E4,

D-97078 Wuerzburg,

Germany.

Tel: +49 (931) 201-71030

Email: Aze...@ukw.de

Matthew Speir

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Jun 4, 2025, 4:59:58 PM6/4/25

to Azeem, Muhammad, Luis Nassar, gen...@soe.ucsc.edu

Hello, Muhammad.

We're having a hard time replicating this issue. Selecting the human hg38 assembly and the "RefSeq All" table for the "NCBI RefSeq" track brings up the output format option "Selected fields from primary and related tables". I tested this on our main site (https://genome.ucsc.edu/) and both our European (https://genome-euro.ucsc.edu/) and Asian (https://genome-asia.ucsc.edu/) mirrors, and it appeared to be functioning as expected.

Can you double-check the URL you are using to access the Genome Browser? Does it match one of the three I listed above? If so, can you provide a session that demonstrates the problem?

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

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/a66a1606a1284596879c5dce5c7a4a10%40ukw.de.

Azeem, Muhammad

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Jun 5, 2025, 12:12:00 PM6/5/25

to Matthew Speir, gen...@soe.ucsc.edu, Luis Nassar

Hi Matthew

Please have a look again on the extended screenshot of my tab, showing the URL and also the available output options. Still I don’t see the “Selected fields from primary and related tables” output format.

I am not very confused why it is happening here but not in your case. I used the same link which mentioned.

I will be looking forward if you can provide me with any solution. Thank you.

Best regards,

============================

Dr. Muhammad Azeem

Gerardo Perez

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Jun 9, 2025, 9:09:07 PM6/9/25

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Hello, Muhammad.

Thank you for providing the screenshots.

It appears that the Intersection feature with KnownGene is currently enabled, which disables the “selected fields from primary and related tables” option in the Table Browser.

To re-enable this option, click the Clear button next to the Intersection section. This should restore access to the “selected fields from primary and related tables” option.

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

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/bb9e87db93524f97ba6d29c77f9a896a%40ukw.de.

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