alu in hg38

[Zachary L Dwight]

Hey UCSC ~

First, your stuff is awesome.

Second, if I download HG38 for Chr22 from your site, does it include all ALU elements?  Or is it only a factor of a true ALU total? 

Thanks!

Zachary Dwight
Scientific Software Manager
Pathology | University of Utah

[Cath Tyner]

Hello Zachary,

Thank you for contacting the UCSC Genome Browser support team. 

You can use the Table Browser to download your regions of interest:

http://genome.ucsc.edu/cgi-bin/hgTables

Select the following options in the Table Browser configuration. For this example, I'll use the hg38 assembly:

clade: mammal, genome: human, assembly: hg38

group: repeats, track: RepeatMasker

table: rmsk

region: genome

filter: repFamily does match "Alu" (without the quotes)

You can then choose whichever fields you would like to output. 

To see output in the browser, leave the "output file" field blank, otherwise, adding a file name will cause the output to download. 

You can see the description page for this track by going to the browser and click on the name of the track.

For example, hg38:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=rmsk

On the track description page, you can see that these data are a bit old, they were last updated 2014-01-10.

Since these data have not been updated since 2014, it's possible that newer elements have been added. 

At the time, I believe all Alu elements were included, not a sub-set. To verify, it is probably best to contact the source:

The source of the data is the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI).

http://www.girinst.org/repbase/update/index.html

gi...@girinst.org

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

​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 help: Email

 genom...@soe.ucsc.edu

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

  * Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

--

---
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 post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/F5105CB1B9FF1E4685827B25A3C2B490D4AF7781%40X-MB1.xds.umail.utah.edu.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.