Hi Jen,

Thanks a lot for your reply. But I think you misuderstood my question. I will reformulate it given examples.

I have initially (because I am doing just preliminary analysis) 70 blat hits corresponding to different coordinates in the pig genome.
What I would like to have is the flanking region in both direction between these blat hits. I am not working with gene (or introns and exons).

For example:

Imagine that this symbol ########## corrsponds to my blat hit  
and this symbol -------------------- corresponds to flanking regions

I have initially ##########
and I would like to obtain  -------------------- ########## --------------------

In numbers:

I have: chr14 64969084 64969603

I would like to have chr14 64962084 64976603
(This will correspont to the first coorditane minus 7000 and the last coordinate plus 7000)

What I got using "Get Flanks" and using the parameters
"Region:" Whole feature
"Location of the flanking region/s:" Both
"Offset" 0
"Length of the flanking region(s):" 7000

chr146496208464969084
chr146496960364976603

Is there a way of merging the above coorditates to come with what I need?

Thanks a lot for your help,

All the best,
Fabricia.


De: Jennifer Jackson <jen@bx.psu.edu>
Para: Fabricia Nascimento <nascimentoff@yahoo.com.br>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Enviadas: Quinta-feira, 3 de Maio de 2012 4:25
Assunto: Re: [galaxy-user] Get flanks (version 1.0.0)

Hello Fabricia,

You are probably running the tool like this, correct? This lumps the
upstream flank and downstream flank ends to create one interval:

"Region:" Whole feature
"Location of the flanking region/s:" Both
"Offset" 0
"Length of the flanking region(s):" 7000

Instead, run the tool in twice to extract upstream and downstream
regions into distinct intervals:

Run 1
"Region:" Whole feature
"Location of the flanking region/s:" Upstream
"Offset" 0
"Length of the flanking region(s):" 7000

Run 2
"Region:" Whole feature
"Location of the flanking region/s:" Downstream
"Offset" 0
"Length of the flanking region(s):" 7000

If your question has been misunderstood, please let us know,

Best,

Jen
Galaxy team


On 5/2/12 5:51 PM, Fabricia Nascimento wrote:
> HI,
>
> I am very new to genomic data analysis and I need to get some upstream
> and downstream of some chromosome regions of the pig genome. I have
> about 70 blat hits of a query of ca 100aa. I need to get 7000
> nucleotides both upstream and downstream of this 100aa region.
> I have tried to use Get flanks to get the "new" coordinates... bus
> instead of generating coordinates which would correspond to about 14000
> nucleotides, it generates one coordinate for the upstream region and
> them another one for the downstream region.
> Is there a way of doing what I need using Galaxy?
>
> I would appreciate any help!
>
> Thanks a lot!
>
> All the best,
> Fabricia.
>
>
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--
Jennifer Jackson
http://galaxyproject.org