Get DNA in Window tool?

[Dolan, Emma]

Hi UCSC Genome team, 

I’m having an issue with the Get DNA in Window tool for hg38. When request DNA sequences for Chromosome X (screenshot below), it returns results for Chromosome 2. In the hg19 version of this tool, I can easily just request a specific base range, but the hg38 tool seems to always cause me trouble. Can you offer any guidance? 

Thanks so much!

Emma Dolan, Ph.D. (she/her)

Postdoctoral Scholar | UCSF

Feng Lab | Radiation Oncology

Ashworth Lab | Cancer Center

[Luis Nassar]

Hi, Emma.

The issue we see with your screenshot is that for hg38 the position is only "chrX:67,774,500". We require this to be a range, e.g., "chrX:67,774,500-chrX:67,774,510". When it isn't a range, the browser logic shows you the last position in that browser, which can lead to unpredictable behavior.

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Lou Nassar
UCSC Genomics Institute

[Dolan, Emma]

Hi Luis, 

Thanks for this reply! Actually when I use a range query, the results are also wrong. Every time I use a range query in the hg38 Get DNA in Window tool, it returns "# No results returned from query.” What do you recommend?

Emma

From: Luis Nassar <lrna...@ucsc.edu>
Date: Tuesday, April 7, 2026 at 9:53 AM
To: Dolan, Emma <emma....@ucsf.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Get DNA in Window tool?

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[Hiram Clawson]

Please provide an example range position you are using.

--Hiram

On 4/7/26 10:13 AM, 'Dolan, Emma' via UCSC Genome Browser Public Support wrote:
> Hi Luis,
> Thanks for this reply! Actually when I use a range query, the results are also wrong. Every time I use a range query in the hg38 Get DNA in Window tool, it returns "# No results returned from query.” What do you recommend?
> Emma
>
>
> From: Luis Nassar <lrna...@ucsc.edu>
> Date: Tuesday, April 7, 2026 at 9:53 AM
> To: Dolan, Emma <emma....@ucsf.edu>
> Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
> Subject: Re: [genome] Get DNA in Window tool?
>
> This Message Is From an External Sender
> This message came from outside your organization.
>
> Hi, Emma.
>
> The issue we see with your screenshot is that for hg38 the position is only "chrX:67,774,500". We require this to be a range, e.g., "chrX:67,774,500-chrX:67,774,510". When it isn't a range, the browser logic shows you the last position in that browser, which can lead to unpredictable behavior.
>

> On Fri, Apr 3, 2026 at 2:00 PM 'Dolan, Emma' via UCSC Genome Browser Public Support <gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>> wrote:
> Hi UCSC Genome team,

> I’m having an issue with the Get DNA in Window<https://urldefense.com/v3/__https://genome.ucsc.edu/cgi-bin/hgc?hgsid=3336170799_52PPRM07i9UewGsNvEwrqXMpuzJj&o=14565265&g=getDna&i=nssv659873&c=chr2&l=14565265&r=14569487&strand=*2B&table=dgvSupporting__;JQ!!LQC6Cpwp!oFG5Abtfvbxd2MbpmdqaAAqqL4a79A_dOfwPQE-JXP8Z9dylKw5DXfBg3m9FW9QWLUGw7YNk3RVrDUeVB85-MA$> tool for hg38. When request DNA sequences for Chromosome X (screenshot below), it returns results for Chromosome 2. In the hg19 version of this tool, I can easily just request a specific base range, but the hg38 tool seems to always cause me trouble. Can you offer any guidance?
> Thanks so much!
>
> [image.png]
>
> [image.png]

> Emma Dolan, Ph.D. (she/her)
> Postdoctoral Scholar | UCSF
> Feng Lab | Radiation Oncology
> Ashworth Lab | Cancer Center
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> I hope this is helpful. Please include gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu> in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu<mailto:genom...@soe.ucsc.edu>.

[Dolan, Emma]

Sure, I’ve tried chrX:67,740,897-67,747,705 just now and received # No results returned from query. I have tried using Firefox, Safari, and Chrome browsers. 

Emma

From: Hiram Clawson <hi...@soe.ucsc.edu>
Date: Tuesday, April 7, 2026 at 10:57 AM
To: Dolan, Emma <emma....@ucsf.edu>, Luis Nassar <lrna...@ucsc.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Get DNA in Window tool?

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[Christopher Lee]

Hi Emma,

Are you first clicking on an item in a track, clicking the "View DNA for this feature" link and then entering your coordinates in? If instead of doing that, from the main tracks image, you use the keyboard shortcut 'vd' or "View -> DNA Sequence" in the top blue menu bar do you have any problems with entering coordinates?

I think there is a sort of UX bug here where there are two different paths through to the get dna feature that is not obvious.

Thanks,

Christopher Lee

UCSC Genomics Institute

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[Christopher Lee]

Great, however we still want to know how you got that link, did you just google "how to get DNA from UCSC" or something? We try our best to fix these things.

Also what and how often do you need to look up sequences? You can consider our rest api, the table browser, or simply downloading the full sequence data (800mb) and using the command line program twoBitToFa to extract specific sequences:

https://genome.ucsc.edu/FAQ/FAQdownloads.html#download1

On Tue, Apr 7, 2026 at 11:47 AM Dolan, Emma <emma....@ucsf.edu> wrote:

Ah interesting! When I use the tool from the top blue bar, it appears to work. My previous failures were using the tool at this web link, which has different sequence retrieval options. I think using the tool from the blue toolbar has solved the problem! Thanks so much!

Emma

[Dolan, Emma]

Because I didn’t previously know that the tool was built into the blue toolbar, I typically find the Get DNA in Window tool by searching “Get DNA in Window hg38” or “Get DNA in Window hg19” into a google search. My search results give me this site and this site. 

Regarding other methods for retrieving DNA sequences, I appreciate these suggestions! I don’t have any coding skills, so that typically limits my abilities. But I’ll take a look at these suggestions and see what might be approachable for me. 

Thanks again for the help! 

[Dolan, Emma]

Ah interesting! When I use the tool from the top blue bar, it appears to work. My previous failures were using the tool at this web link, which has different sequence retrieval options. I think using the tool from the blue toolbar has solved the problem! Thanks so much!

Emma

[Christopher Lee]

Many thank this is good to know!

Please let us know if you have any further questions and we will let you know if we get a fix out for those two bugs you found