[Genome] Help!

[Brooke Rhead]

Hello Wen-Xin,

You can get summary information on Genome Browser tracks using the Table 
Browser.  To do so, hit the "Tables" link in the blue bar at the top of 
the page, and make the following selections:

clade: vertebrate
genome: human
assembly: March 2006 (or whichever assembly you are using)
group: variation and repeats
track: RepeatMasker or Simple Repeats (whichever is of interest)
table: rmsk or simpleRepeat
region: genome

Then hit the "summary/statistics" button at the bottom of the page.  You 
  should get a list of statistics about the track, including an "item 
count", which is the number of items in a track, and "item bases", which 
is the number of genomic bases covered by items in the track.

You can also go back and use the filter button to limit the types of 
repeats that are counted in the summary.  For instance, if you are using 
the RepeatMasker track, you can hit the "filter: create" button, and 
then choose to limit your search so that "repClass does match SINE" 
(this is just an example -- you might want to use some other kind of 
filter).

I hope this is helpful.  If you have further questions please feel free 
to write to this mailing list again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



ZhengWenXin wrote:
> Dear Prof., Would you please help me to resolve a problem about the
> repeat track of the UCSC genome browser?
> I’m interested in the repeat of the human genome. Though the Repeat
track, I could easily find what repeats were aligned along the sequence.
But would you please tell me the occurrence frequencies of short repeats
in the whole human genome?
> Thank you very much! Your help will be greatly appreciated.
> Best wishes,
> WenXin Zheng
>  
>  
>  
>  
> Wen-Xin Zheng, PhD candidate
> Bioinformatics Center
> Tianjin University
> Tianjin 300072
> China
> Fax: +86-22-27402697
> Website: http://tubic.tju.edu.cn
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