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João Fadista
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@joao-fadista-1942
Last seen 10.2 years ago
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: s?b 16-12-2006 18:37
Para: Ann Zweig
Assunto: RE: [Genome] EST?s mapped to a known structural variation
region
Hello Jo?o,
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=""/>
Jo?o 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
>
> Jo?o Fadista
> Ph.d. student
>
>
>
> Danish Institute of Agricultural Sciences
> Research Centre Foulum
> Dept. of Genetics and Biotechnology
> Blichers All? 20, P.O. BOX 50
> DK-8830 Tjele
>
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> Direct: +45 8999 8999
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