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

[Hiram Clawson]

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/>