[Genome] 3' fasta sequence

[Brooke Rhead]

Hi Lana,

Identifiers in the "UCSC Genes" track have a version number at the end 
(which are all currently ".1").  So, instead of entering "uc002fgk", 
enter "uc002fgk.1".

If 8 of your 10 identifiers have matches, you should be seeing fasta 
sequence for at least the 8 successful matches.  Be sure that "region: 
genome" is selected in the Table Browser.  Otherwise, output will be 
restricted to the region specified in the position box.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Lana Schaffer wrote:
> 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