[Gong, Shiaoching]

Dear Sir/Madam,

Good afternoon.

I could not find BAC clones in UCSC website. Could you please advise?
Thanks,

Shiaoching

[Gong, Shiaoching]

Thanks, I found the BAC clones. Could you please let me know what is the difference between blue and green clones?

Thanks!

[Cath Tyner]

Hello Shiaoching,

Thank you for using the UCSC Genome Browser and for submitting your question regarding the meaning of the green and blue Clone Ends track. We will update the description page soon to indicate the meaning of the color as it related to strand; blue is for the forward (+) strand and green indicates the reverse (-) strand.

Description pages for Clone Ends tracks:

• Human hg38
• Mouse mm10
  

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

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private data help: Email

 genom...@soe.ucsc.edu

UCSC Genome Browser Announcements List (email alerts for new data & software):

  * Subscribe: Email genome-annou...@soe.ucsc.edu 
  * Unsubscribe: Email genome-announ...@soe.ucsc.edu

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Ryan Kevin (GUY'S AND ST THOMAS' NHS FOUNDATION TRUST)]

Would just like to check if there is a difference between the database used by the live Table browser compared to the database version which can be downloaded. I noticed that there are a number of extra transcripts being pulled up by the Table browser when I search refGene for the gene AASDH compared to if I do the same search using the downloaded database. It says in the help that occasionally there can be a lag in the release of the downloaded version. Is this the reason for the differences that I see for this gene.
Many thanks
Kevin

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[Brian Lee]

Dear Kevin,

Thank you for using the UCSC Genome Browser and your question about possible differences between the Table Browser and downloadable files.

You are correct there are can be differences between the two, but there should be a delay of only about a week between the data that is available on the Table Browser and the data that is updated on the hgdownload server and our public MySQL server. Each Sunday there is an automatic rsync of the current MySQL data available through the Table Browser to our hgdownload server, which is then also copied nightly to our public genome-mysql server.

Please note that since the MySQL data on our site available through the Table Browser can be constantly updating, by the day following the weekend rsync has occurred, new additional information could have been added. For example, you should not see the same differences between the two locations after 8 days around a specific gene, unless even newer annotation differences have been added. If you do see persistent differences over a prolonged time, please do bring the specific example to our attention with dates of access.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply toge...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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