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

[Heather Trumbower]

Joao:

Data on our test server may be undergoing edits and/or reviews.  In this 
case, I'm hoping to find additional cross-links to add to the Redon data.
Past that, our review team will look at this data.

At this time I would recommend the hg17 data to you.   I am working with 
collaborators to provide additional SV data on hg18, I hope to have this 
on our regular server sometime in January.

Heather


On Mon, 18 Dec 2006, João Fadista wrote:

> 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/>
>>
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>