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
--
---
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 on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAPrkkgY%2BtBqKcGqFzfO9uiV%3DGeJmTKarA0%3D6X3bC58H1TM%2BmYw%40mail.gmail.com.
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.
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:
>> <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://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:
>>> 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&d=DwICaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9LD0EGBR5hruR-2KTr2ZQ&m=sXAqd9IYnx4Xgo0CK3TGEgYFedE7mossNLgDR0uo7ZvIygLgyTKCeBPym_i0p9oc&s=ZE4zKiwJOU_cZ5R18JQOEijos9-RX3n5gCJYmAp02lg&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=>
>>> .
>>>
>>
>