RE: [Genome] EST´s mapped to a known structural variation region

[João Fadista]

Dear Heather Trumbower,
 
Thanks for the useful information. I have 2 more questions if you don´t mind. So what does it mean to be in your test server? If I want to map my EST´s to a region of known structural variation should I use the Redon data
in the hg18 or other data from the hg17?
 
Kind regards,
João Fadista

________________________________

De: Heather Trumbower [mailto:heather at soe.ucsc.edu]
Enviada: seg 18-12-2006 17:02
Para: João Fadista
Cc: Hiram Clawson; genome at soe.ucsc.edu
Assunto: RE: [Genome] EST´s mapped to a known structural variation region



Joao:

The Redon data is just recently published and is currently only available
on our test server, which is http://genome-test.cse.ucsc.edu <http://genome-test.cse.ucsc.edu/> .   In
addition to being available in the May 2004 (hg17) assembly along with
other SV data, the Redon data is the first SV data available for the March
2006 (hg18) assembly.  It is currently in a track called "Redon CNPs".
This track will be renamed to "Structural Var" as we receive additional SV
data for hg18.

The reference for this data is:
Redon, R., Ishikawa, S., Fitch, K., Feuk, L., Perry, G., Andrews, T.,
Fiegler, H., Lee, C., Jones, K., Scherer, S., Hurles, M. et al. Global
variation in copy number in the human genome. Nature 444(7118), 444-454
(2006).

Please let me know if you have any further questions on the Redon et.al.
SV data.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Sun, 17 Dec 2006, João Fadista wrote:

> Hi Hiram Clawson,
>
> Thanks for the information.
> Concerning the intersection of my Custom Track with the Structural Variation track,
> I am not able to choose the data table from "Redon analysis of HapMap data". Isn´t
> available yet?
>
> Kind regards,
> João Fadista
>
>
> ________________________________
>
> De: Hiram Clawson [mailto:hiram at soe.ucsc.edu]
> Enviada: dom 17-12-2006 13:54
> Para: João Fadista
> Cc: 'genome at soe.ucsc.edu' genome
> Assunto: Re: [Genome] EST´s mapped to a known structural variation region
>
>
>
> Good Morning João:
>
> browser position is only a starting location for the first
> time after loading your track.  After that, you browse through
> the genome to look at any location.
>
> --Hiram
>
> On 2006 Dec 17, , at 3:59 AM, João Fadista wrote:
>
>> Dear Ann Zweig,
>>
>> I have a doubt about the input format file. You said that I can put my
>> data in this format:
>>
>> 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
>>
>> But what should I write in "browser position..." if my EST´s are
>> mapped all across the genome?
>>
>> Kind regards,
>> João Fadista
>>
>> ________________________________
>>
>> De: Ann Zweig [mailto:ann at soe.ucsc.edu]
>> Enviada: sex 15-12-2006 18:46
>> Para: João Fadista
>> Cc: genome at soe.ucsc.edu
>> 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/>  <http://genome.ucsc.edu/>  <http://genome.ucsc.edu/>
>
>
>
>
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