[Genome] downloads for Variation and Repeats tracks

[Dmitry]

Hi All,

I figured out the CXCL2 part.
This is a negatively aligned gene so the 22xCA became 22XGT, which is
there.
But the second question stands.
Why tandem repeats less than 15 elements are not reported and how to
retrieve them?

Thank you

Dmitry

-----Original Message-----
From: Dmitry [mailto:dgrigor1 at jhmi.edu] 
Sent: Monday, April 09, 2007 12:03 PM
To: 'Ann Zweig'
Cc: 'genome at soe.ucsc.edu'
Subject: RE: [Genome] downloads for Variation and Repeats tracks

Hi All,

The provided Variation and Repeats datasets are very useful, thank you.
But unfortunately I noticed that there a lot of tandem repeats that are
not reported.

For example in the 2000 bases upstream region of CXCL2 gene there is
22xCA
Chr4  75180980
GTTGAAACACACACACACACACACACACACACACACACACACACACACACACGTGATA ,

which I couldn't find in nether Trf or Microsatellite datasets.

Are those repeats skipped or masked purposely?
If so where can I find unmasked datasets?
Also you are not reporting tandem repeats that have less than 12
components.
Is there a way to retrieve those as well?

Thank you for your help

Dmitry

-----Original Message-----
From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
Sent: Thursday, April 05, 2007 7:35 PM
To: Dmitry
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] downloads for Variation and Repeats tracks

Hello Dmitry,

	You can download the MySQL tables underlying the data from our
download server. 
  Follow the 'Downloads' link from the blue navigation bar on the left
side of 
the home page.  From there, press Human, then under hg18 (or the
assembly you 
are interested in) press Annotation Database.  This directory contains a
file 
for each table in the database.

	You will need to determine the name of the table that supports
the track you 
are interested in. To do this in the genome browser, simply press the
hyperlink 
for the name of the track in the track controls under the display.  In
the URL 
on this page, you will see (usually at the very end), "g=abc".  The
'abc' is the 
name of the table that underlies this track.  This is the table you will
want to 
download from the Download server.

	For example, for the SNP track in the hg18 browser, the table
name is snp126.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


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Dmitry wrote:
> Hi,
>  
> Where can I find and download psl files for the Variation and Repeats
> tracks?
>  
> Thank you
>  
> Dmitry
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome