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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