[Genome] single transcript genes

[Rachel Harte]

Rudy,

There isn't a way to do this directly with the Table Browser. If you have
mySQL installed locally, you can use our mySQL server and use this mySQL
query:

select name from refLink group by name having count(name) = 1;

on the database of interest e.g. hg18 for the most recent human Genome
Browser database.
Here are instruction on how to access this server:
http://genome.ucsc.edu/FAQ/FAQdownloads#download29

The other way that you could do it is to use the Table Browser and select
Genes and Gene Prediction Tracks as the group, RefSeq Genes as the track,
refLink as the table. Then select "selected fields from primary and
related tables" as the output and select just the name field.
The you could use a script to sort and count the occurrences of each gene
in the table e.g.
sort file | uniq -c | sort -nr
where file is your output file from the Table Browser.

Then you can select just those that have a count of 1 which will be at the
top.
I hope that this helps you. Please let us know if you have further
questions.

Rachel
 Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Tue, 19 Dec 2006, Rudy Spangler wrote:

> Hi UCSC folks:
> Is there a way to get from your Table Browser a list of human genes for which only one (1) refseq transcript exists?
> Rudy Spangler
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