[Genome] 3' fasta sequence

[Lana Schaffer]

Hi,
I am trying to input a list and having trouble getting out
The sequences.  I am getting the error message:
Note: 2 of the 10 given identifiers (e.g. uc002fgk) have no match in
table knownGene, field name or in alias table kgAlias, field alias. Try
the "describe table schema" button for more information about the table
and field.
When I try to output the file, then the file is empty.
Lana


-----Original Message-----
From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
Sent: Tuesday, February 12, 2008 3:43 PM
To: Lana Schaffer
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] 3' fasta sequence

Hello Lana,

You can use the Table Browser (the "Tables" link in the blue bar at the 
top of the page) to get fasta sequences.  Choose the track for which you

would like to retrieve sequence, and "outputput format: sequence", then 
hit "get output".

If you are using a "Genes and Gene Predictions" track, you should see an

option on the next page to select genomic, protein or mRNA sequence.  If

you choose to retrieve genomic sequence, there will be additional 
options to retrieve only certain regions of genes, such as 3' UTR Exons.

General instructions for using the Table Browser are here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

If you have additional questions, please feel free to write back to the 
mailing list address.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Lana Schaffer wrote:
> Hi,
> Is there an easy batch query to get the fasta sequence
> Or 3' fasta sequence?
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu 
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome