[BioC] EST´s mapped to a known structural variation region

[João Fadista]

Dear all,
 
The information below is from UCSC genome browser mailing list and it was useful for me. So I post it in this mailing list because first I asked a question to the BioC mailing list, thinking that there was a package to do what I wanted. So here it is the answer to my question: 
 
________________________________

De: 
Enviada: sáb 16-12-2006 18:37
Para: Ann Zweig
Assunto: RE: [Genome] EST´s mapped to a known structural variation region



Hello João,

     There is a Structural Variation track on the previous human genome browser
(hg17, May 2004).  You can create a custom track with the data from your
experiment, then use the Table Browser to intersect your custom track with the
Structural Variation track.

     I will use these three ESTs as an example to show you how to do this:

BI549060   chr7:115495968-115496505
BX098195   chr7:115517846-115520200
AA528379   chr7:115570816-115571048

     First create a custom track with the ESTs.

1. Open the hg17 browser and press the "add custom track" button.
2. Add your data as a custom track in a BED4 format like so:

track name=ESTs description="ESTs from my microarray experiment"
browser position chr7:115493217-115580399
chr7 115495968 115496505 BI549060
chr7 115517846 115520200 BX098195
chr7 115570816 115571048 AA528379


     Now use the Table Browser to intersect your custom track with the
Structural Variation track.

3. Set up the Table Browser options like so:
group = Custom Tracks
track = ESTs (or your Custom Track name)
region = genome

4. Intersect your Custom Track with the Structural Variation track:
press the "create" button next to 'intersection'.  Choose:
group = Variation and Repeats
track = Structural Var
table = Tuzun Fosmids (or whichever data table is most appropriate for your
interest).

Press "submit" to return to the main Table Browser page.

     Now choose your output  type.  If you choose BED, for example, you will get
a BED list of all of your original ESTs that intersect with the Tuzun Fosmids
table.  The output in this example is:

chr7    115517846    115520200    BX098195

     I hope this is helpful to you.  Feel free to write back if you have more
questions.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu <http://genome.ucsc.edu/> 


João Fadista wrote:
> Dear all,
> 
> I have made a microarray experiment with some EST´s (expression sequence tags) and I would like to see if those EST´s are in a  known region of structural variation in the human genome.
> 
> So I was wondering if there is a way, using the UCSC table browser or other application, to input all my EST´s ( their sequence in FASTA format or their positions in the genome) and then retrieve an output file with those that are mapped to a known region of structural variation.
> 
>
> Best regards
>
> João Fadista
> Ph.d. student
>
>
>      
>        Danish Institute of Agricultural Sciences     
> Research Centre Foulum       
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