Overlapping features - species specific

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Overlapping features - species specific

Jayaraman, Pushkala

Hello,

I was wondering if there was a way in which I could specify the species for the overlapping features post-processing function..

When I go to a gene and I find 48 overlapping features for mouse gens, I see rat qtls

How do I avoid that?

 

Im sure you guys have multiple species or even strains, in your mines.. how do you guys handle this??

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 


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Re: Overlapping features - species specific

Julie Sullivan
Hi Pushkala

That shouldn't ever happen! See the docs:

http://intermine.github.io/intermine/org/intermine/bio/postprocess/OverlapUtil.html
"Creates OverlapRelations for overlapping SequenceFeature objects that
are located on the given subject (generally a Chromosome)."

Since the mouse and rat genes are on different chromosomes, the
OverlapUtil will never calculate them as being overlapping.

Can you verify your mouse and rat chromosomes are correct? Or if your
dev webapp is viewable I can take a look.

Julie


On 26/09/13 21:13, Jayaraman, Pushkala wrote:

> Hello,
>
> I was wondering if there was a way in which I could specify the species
> for the overlapping features post-processing function..
>
> When I go to a gene and I find 48 overlapping features for mouse gens, I
> see rat qtls
>
> How do I avoid that?
>
> Im sure you guys have multiple species or even strains, in your mines..
> how do you guys handle this??
>
> Pushkala Jayaraman
>
> Programmer/Analyst - Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> 414-955-2229
>
> http://rgd.mcw.edu
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: Overlapping features - species specific

Jayaraman, Pushkala

So here is what happens,

It lists the genes/qtls from the other specis that are within the same region. .

For eg, if I am looking at a gene or a qtl from the Rat,

It shows me overlapping features, genes/qtls from mouse and human within the equivalent region as that of the rat feature I am looking at

How do I fix that?

Here is a screenshot:

 

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Monday, September 30, 2013 7:13 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [InterMine Dev] Overlapping features - species specific

 

Hi Pushkala

 

That shouldn't ever happen! See the docs:

 

http://intermine.github.io/intermine/org/intermine/bio/postprocess/OverlapUtil.html

"Creates OverlapRelations for overlapping SequenceFeature objects that are located on the given subject (generally a Chromosome)."

 

Since the mouse and rat genes are on different chromosomes, the OverlapUtil will never calculate them as being overlapping.

 

Can you verify your mouse and rat chromosomes are correct? Or if your dev webapp is viewable I can take a look.

 

Julie

 

 

On 26/09/13 21:13, Jayaraman, Pushkala wrote:

> Hello,

> 

> I was wondering if there was a way in which I could specify the

> species for the overlapping features post-processing function..

> 

> When I go to a gene and I find 48 overlapping features for mouse gens,

> I see rat qtls

> 

> How do I avoid that?

> 

> Im sure you guys have multiple species or even strains, in your mines..

> how do you guys handle this??

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst - Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> 414-955-2229

> 

> http://rgd.mcw.edu

> 

> 

> 

> _______________________________________________

> dev mailing list

> [hidden email]

> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

> 


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Re: Overlapping features - species specific

Julie Sullivan
Can you verify your mouse and rat chromosomes are correct?

On 30/09/13 18:39, Jayaraman, Pushkala wrote:

> So here is what happens,
>
> It lists the genes/qtls from the other specis that are within the same
> region. .
>
> For eg, if I am looking at a gene or a qtl from the Rat,
>
> It shows me overlapping features, genes/qtls from mouse and human within
> the equivalent region as that of the rat feature I am looking at
>
> How do I fix that?
>
> Here is a screenshot:
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Monday, September 30, 2013 7:13 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Overlapping features - species specific
>
> Hi Pushkala
>
> That shouldn't ever happen! See the docs:
>
> http://intermine.github.io/intermine/org/intermine/bio/postprocess/OverlapUtil.html
>
> "Creates OverlapRelations for overlapping SequenceFeature objects that
> are located on the given subject (generally a Chromosome)."
>
> Since the mouse and rat genes are on different chromosomes, the
> OverlapUtil will never calculate them as being overlapping.
>
> Can you verify your mouse and rat chromosomes are correct? Or if your
> dev webapp is viewable I can take a look.
>
> Julie
>
> On 26/09/13 21:13, Jayaraman, Pushkala wrote:
>
>  > Hello,
>
>  >
>
>  > I was wondering if there was a way in which I could specify the
>
>  > species for the overlapping features post-processing function..
>
>  >
>
>  > When I go to a gene and I find 48 overlapping features for mouse gens,
>
>  > I see rat qtls
>
>  >
>
>  > How do I avoid that?
>
>  >
>
>  > Im sure you guys have multiple species or even strains, in your mines..
>
>  > how do you guys handle this??
>
>  >
>
>  > Pushkala Jayaraman
>
>  >
>
>  > Programmer/Analyst - Rat Genome Database
>
>  >
>
>  > Human and Molecular Genetics Center
>
>  >
>
>  > Medical College of Wisconsin
>
>  >
>
>  > 414-955-2229
>
>  >
>
>  > http://rgd.mcw.edu
>
>  >
>
>  >
>
>  >
>
>  > _______________________________________________
>
>  > dev mailing list
>
>  > [hidden email] <mailto:[hidden email]>
>
>  > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>  >
>

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[hidden email]
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