[Genome] question about ucsc genome browser?

[Brooke Rhead]

Hello Zd,

You can find the number of non-overlapping RefSeq Genes using the Table 
Browser and the tools at Galaxy (which is run by Penn State University). 
  I will walk you through the steps.

In the Table Browser (click on "Tables" in the blue bar at the top of 
the page), select the clade, genome, and assembly you wish to work with. 
  Then choose:

group: Genes and Gene Prediction Tracks
track: RefSeq Genes
table: refGene
region: genome
output format: all fields from selected table

Select the box next to "Send output to Galaxy".  Now hit "get output" 
and then "send query to Galaxy".  You will be taken to the Galaxy web 
site, where you can use their tools to manipulate data.  You should see 
the data from the RefSeq Genes table listed on the right side of the 
page, and a list of tools on the left side.

Now click on the "Operate on Genomic Intervals" group in the tools 
section and choose to "Merge the overlapping intervals of a query". 
Select the refGene table in the drop-down menu and hit "execute".  Once 
the job has run, you can expand the item on the right-hand side and see 
a count of the items.  For the human (hg18) database, the total number 
of genes in the refGene table before merging is 25,931, and after 
merging it is 17,960.

If you would like to see the merged data as a custom track in the Genome 
Browser, click on the Galaxy link to "display at UCSC main".

I hope this helps.  If you have further questions, please feel free to 
write back to us at this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



zxu wrote:
> What is the total number of unique Ref seq genes (no overlapping exons) in the
> genome?  how can I get this number?
> 
> zd
> 
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