[Genome] Sequence retrieval

[Archana Thakkapallayil]

Hello Mia,

When you upload the genomic coordinates using the 'defined regions' 
feature in the Table Browser and retrieve the sequences by setting the 
'table:gold', you are actually getting the sequences for the entire 
contigs that are included in your region of interest. In order to get 
the sequences for your genomic coordinates, you could first upload your 
BED file as a custom track, using the button "add custom tracks" on the 
Genome Browser gateway.

The custom track user's guide is here:
http://www.genome.ucsc.edu/goldenPath/help/customTrack.html

Then on the 'Table Browser', select 'Custom Tracks' as group and the 
corresponding track and table. Then choose 'region: genome'; 'output 
format: sequence' and hit 'get output'.

I hope that this helps you. Please let us know if you have further 
questions.

Regards,

Archana
UCSC Genome Bioinformatics Group


Sung, Myong-Hee (NIH/NCI) [E] wrote:
> Hi,
>
> I'm trying to retrieve genomic sequences by their BED format genomic
> coordinates.  I uploaded my file of genomic coordinates onto the
> 'defined regions' in Table Browser and specified settings (Mouse; Feb
> 2006; All Tables; mm8; gold; sequence output).  But what I get is
> genomic sequences covering much larger regions than my chromosome
> coordinates, perhaps something that could be contigs.  I've tried
> querying a single region but had the same problem.  My regions are
> genomic, not necessarily promoter or coding regions.
> I've browsed through your Q&A but couldn't figure it out.  I'm guessing
> I should specify certain retrieval settings differently?  What will do
> the trick?
>
> Thanks in advance.
>
> Mia
>
> 	Myong-Hee Sung, Ph.D.
> 	Laboratory of Receptor Biology and Gene Expression
> 	National Cancer Institute, NIH
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> 	Bethesda, MD 20892
>
> 	Office: 301-402-0364
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> 	email: sungm at mail.nih.gov
> 	http://ccr.cancer.gov/staff/staff.asp?profileid=11633
>
>
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