[Genome] UCSC known genes and TSS

[Kayla Smith]

Hello Maria,

Yes you can use the txStart site as a TSS.   We use RNA evidence to 
support the choice of txStart.  Here is a link to our Known Genes methods:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr7&g=knownGene

You could also use ensembl TSSs from us if you didn't want to use the 
UCSC genes.  The table name for the Ensembl Genes is "ensGene".

Additionally we have two existing TSS tracks on our hg18 browser:

1.  SwitchGear TSS
2.  Eponine TSS

They are found under the "Expression and Regulation" subsection of the 
browser track controls.

I hope this helps get you started.  Please don't hesitate to contact us 
again if your require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Maria Astrom wrote:
> Dear Friends,
> I want to use the predicted TSSs for hg18 genome for my project. Is it appropriate to use the TxStart of UCSC known genes track ?
> Or are there any drawbacks ?
>  
>  
>  ThanksSincerely,Maria
> 
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