Sk1 Genome addition

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Carolyn Milano

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Nov 18, 2021, 3:08:12 PM11/18/21
to gen...@soe.ucsc.edu, Andreas Hochwagen
Hello,

I would like to use the UCSC genome browser to look at the saccharomyces cerevisiae strain SK1
The accession number is GCA_002250225.1

Would you be able to add this?

Thank you,
Carolyn Milano 

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Carolyn R. Milano, Ph.D.
Hochwagen Lab 
Department of Biology
New York University
1009 Silver Center
100 Washington Square East
New York, NY 10003-6688

Gerardo Perez

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Nov 19, 2021, 3:52:28 PM11/19/21
to Carolyn Milano, genome, Andreas Hochwagen

Hello, Carolyn.

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

We offer this saccharomyces cerevisiae strain SK1 assembly (GCA_002250225.1) as an assembly hub:
https://genome.ucsc.edu/h/GCA_002250225.1

The supporting download files can be found here:
https://hgdownload.soe.ucsc.edu/hubs/GCA/002/250/225/GCA_002250225.1/

You can read about assembly hubs here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly.

I hope this is helpful. Please include 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.

Gerardo Perez
UCSC Genomics Institute


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Carolyn Milano

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Nov 30, 2021, 8:49:52 PM11/30/21
to Gerardo Perez, gen...@soe.ucsc.edu, Andreas Hochwagen
Thank you very much Gerardo, unfortunately I am still having trouble using this assembly hub. 

My files are properly in the 2bit format and UCSC hub accepts and adds it, but my tracks are empty and instead of the data it displays "No Data". 

I suspect this might be because the SK1 assembly available on UCSC doesn't have the genome organized into chromosomes, but instead it is organized by assembly number, short sequences that do not map back to chromosomes.

I need the SK1 assembly to be showing chromosomes instead of assembly numbers, but I can not figure out how to do that. 
I can't find the solution to this online, would you know how I can reorganize the assembly hub to display chromosomes instead of assembly numbers? 
I am trying to do this for a paper we have under review at the request of the journal.  
If you can point me to some directions on this, I would greatly appreciate it.

All the best,
Carolyn

 

Hiram Clawson

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Nov 30, 2021, 8:54:32 PM11/30/21
to Carolyn Milano, Gerardo Perez, gen...@soe.ucsc.edu, Andreas Hochwagen
Good Evening Carolyn, can you clarify which genome assembly you are referring to ?
What is the GCA or GCF accession identifier ?

--Hiram
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__genome.ucsc.edu_h_GCA-5F002250225.1&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9LD0EGBR5hruR-2KTr2ZQ&m=MQrW1R6jaBwFnLik6vhrKqBMCJFD9zXi912FiviPdqnxWzzZ0M9stkuNPJYoabv-&s=JZ5WNs2jj183-fYH7WnElCYoaR_Vg4u4XQtlB5bjK6I&e=>
>>
>> The supporting download files can be found here:
>> https://hgdownload.soe.ucsc.edu/hubs/GCA/002/250/225/GCA_002250225.1/
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hgdownload.soe.ucsc.edu_hubs_GCA_002_250_225_GCA-5F002250225.1_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9LD0EGBR5hruR-2KTr2ZQ&m=MQrW1R6jaBwFnLik6vhrKqBMCJFD9zXi912FiviPdqnxWzzZ0M9stkuNPJYoabv-&s=Wo1jnG3CQ5_0IimXUcYOCclyodj4cEyf7AIxt6d6PGE&e=>
>>
>> You can read about assembly hubs here:
>> http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__genome.ucsc.edu_goldenPath_help_hgTrackHubHelp.html-23Assembly&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9LD0EGBR5hruR-2KTr2ZQ&m=MQrW1R6jaBwFnLik6vhrKqBMCJFD9zXi912FiviPdqnxWzzZ0M9stkuNPJYoabv-&s=9v9Kkgb_AhVXMWkPdyMDKovDKE2PEHlY4vRQHteVEtU&e=>
>> .
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_a_soe.ucsc.edu_d_msgid_genome_CAPrkkgY-252BtBqKcGqFzfO9uiV-253DGeJmTKarA0-253D6X3bC58H1TM-252BmYw-2540mail.gmail.com-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dfooter&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9LD0EGBR5hruR-2KTr2ZQ&m=MQrW1R6jaBwFnLik6vhrKqBMCJFD9zXi912FiviPdqnxWzzZ0M9stkuNPJYoabv-&s=MBQ5vPh0ofXirqE57-L_FtS0eBYUNSMLoTCqx2_TilU&e=>
>>> .
>>>
>>
>

Maximilian Haeussler

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Dec 1, 2021, 3:32:14 AM12/1/21
to Hiram Clawson, Carolyn Milano, Gerardo Perez, UCSC Genome Browser Discussion List, Andreas Hochwagen
Hi Carolyn,

the only "chromosome-level" assembly of SK1 that I can find at NCBI is GCA_002057885.1. Did you use this one for your result files? Maybe you meant this assembly and not the one that you requested, GCA_002250225.1 ?

best
Max

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/e4b34f60-d978-4623-a598-211f5fd56bf9%40soe.ucsc.edu.

Carolyn Milano

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Dec 1, 2021, 11:59:43 AM12/1/21
to Hiram Clawson, Carolyn Milano, Gerardo Perez, gen...@soe.ucsc.edu, Andreas Hochwagen
Dear Hiram,
I am using the SK1 assembly (GCA_002250225.1) as an assembly hub:
https://genome.ucsc.edu/h/GCA_002250225.1

On Tue, Nov 30, 2021, 8:54 PM Hiram Clawson <hi...@soe.ucsc.edu> wrote:
Good Evening Carolyn, can you clarify which genome assembly you are referring to ?
What is the GCA or GCF accession identifier ?

--Hiram

On 11/30/21 5:20 PM, Carolyn Milano wrote:
> Thank you very much Gerardo, unfortunately I am still having trouble using
> this assembly hub.
>
> My files are properly in the 2bit format and UCSC hub accepts and adds it,
> but my tracks are empty and instead of the data it displays "No Data".
>
> I suspect this might be because the SK1 assembly available on UCSC doesn't
> have the genome organized into chromosomes, but instead it is organized by
> assembly number, short sequences that do not map back to chromosomes.
>
> I need the SK1 assembly to be showing chromosomes instead of assembly
> numbers, but I can not figure out how to do that.
> I can't find the solution to this online, would you know how I can
> reorganize the assembly hub to display chromosomes instead of assembly
> numbers?
> I am trying to do this for a paper we have under review at the request of
> the journal.
> If you can point me to some directions on this, I would greatly appreciate
> it.
>
> All the best,
> Carolyn
>
>
>
> On Fri, Nov 19, 2021 at 3:52 PM Gerardo Perez <gpe...@ucsc.edu> wrote:
>
>> Hello, Carolyn.
>>
>> Thank you for your interest in the Genome Browser and sending your inquiry.
>>
>> We offer this saccharomyces cerevisiae strain SK1 assembly
>> (GCA_002250225.1) as an assembly hub:
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