GFF question

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GFF question

David Breimann
I'm trying to figure out how to use relative coordinates in a GFF file
under GBrowse.

Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
its sequence and annotations into GBrowse.

Now I would like to focus (mentally... not visually :)) on a specific
region within this chromosome ("region1") of 100kb - let's say
chr1:100001-200000, and use a GFF file
(region1.gff) with coordinate relative to region1, e.g. a feature in
region.gff with coordinates 1 100 will be displayed on chr1
100001-100100.

Is this possible?

I hope I was clear...

Thank you ,
David

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Re: GFF question

Jayaraman, Pushkala
Are you trying to ask whether you can visualize a region within a
chromosome while having features on the chromosome as well..
:)

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: David Breimann [mailto:[hidden email]]
Sent: Thursday, July 08, 2010 12:33 PM
To: [hidden email]
Subject: [Gmod-gbrowse] GFF question

I'm trying to figure out how to use relative coordinates in a GFF file
under GBrowse.

Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
its sequence and annotations into GBrowse.

Now I would like to focus (mentally... not visually :)) on a specific
region within this chromosome ("region1") of 100kb - let's say
chr1:100001-200000, and use a GFF file
(region1.gff) with coordinate relative to region1, e.g. a feature in
region.gff with coordinates 1 100 will be displayed on chr1
100001-100100.

Is this possible?

I hope I was clear...

Thank you ,
David

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Fwd: GFF question

David Breimann
---------- Forwarded message ----------
From: David Breimann <[hidden email]>
Date: Thu, Jul 8, 2010 at 9:59 PM
Subject: Re: [Gmod-gbrowse] GFF question
To: "Jayaraman, Pushkala" <[hidden email]>


I'm not sure I understand you...
Maybe a good example will be a chromosome and a gene within it.
I have a GFF for some chromosome listing all the genes within it.
Can I use features with coordinate relative to some specific gene?
(e.g. introns/exons with positions relative to the gene start instead
of absolute positions in the chromosome).

On Thu, Jul 8, 2010 at 9:14 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Are you trying to ask whether you can visualize a region within a
> chromosome while having features on the chromosome as well..
> :)
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: David Breimann [mailto:[hidden email]]
> Sent: Thursday, July 08, 2010 12:33 PM
> To: [hidden email]
> Subject: [Gmod-gbrowse] GFF question
>
> I'm trying to figure out how to use relative coordinates in a GFF file
> under GBrowse.
>
> Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
> its sequence and annotations into GBrowse.
>
> Now I would like to focus (mentally... not visually :)) on a specific
> region within this chromosome ("region1") of 100kb - let's say
> chr1:100001-200000, and use a GFF file
> (region1.gff) with coordinate relative to region1, e.g. a feature in
> region.gff with coordinates 1 100 will be displayed on chr1
> 100001-100100.
>
> Is this possible?
>
> I hope I was clear...
>
> Thank you ,
> David
>
> ------------------------------------------------------------------------
> ------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: GFF question

Jayaraman, Pushkala
In reply to this post by Jayaraman, Pushkala
Aah! No. That you wouldn't be able to do..
Although, one may be able to show that in an "init_code" ... just may
be.. im sure people on the forum will have something interesting to say
about this..

Although, the glyphs also have a feature wherein you can activate "box
subparts" so mousing over a part of the gene which has an exon, will
show you coordinates for that exon (relative to the chromosome, not the
gene) in that gene. The search tab will also be able to search for exons
coordinates (relative to the chromosome) instead of gene coordinates..
given that your gff3 file has it..
Gbrowse2 SeqFeature Store allows users that depth in storage..but Im
sure, coordinates relative to gene is doable in the init_code of the
data source conf file.. never tried it though..    

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: David Breimann [mailto:[hidden email]]
Sent: Thursday, July 08, 2010 1:59 PM
To: Jayaraman, Pushkala
Subject: Re: [Gmod-gbrowse] GFF question

I'm not sure I understand you...
Maybe a good example will be a chromosome and a gene within it.
I have a GFF for some chromosome listing all the genes within it.
Can I use features with coordinate relative to some specific gene?
(e.g. introns/exons with positions relative to the gene start instead
of absolute positions in the chromosome).

On Thu, Jul 8, 2010 at 9:14 PM, Jayaraman, Pushkala <[hidden email]>
wrote:

> Are you trying to ask whether you can visualize a region within a
> chromosome while having features on the chromosome as well..
> :)
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: David Breimann [mailto:[hidden email]]
> Sent: Thursday, July 08, 2010 12:33 PM
> To: [hidden email]
> Subject: [Gmod-gbrowse] GFF question
>
> I'm trying to figure out how to use relative coordinates in a GFF file
> under GBrowse.
>
> Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
> its sequence and annotations into GBrowse.
>
> Now I would like to focus (mentally... not visually :)) on a specific
> region within this chromosome ("region1") of 100kb - let's say
> chr1:100001-200000, and use a GFF file
> (region1.gff) with coordinate relative to region1, e.g. a feature in
> region.gff with coordinates 1 100 will be displayed on chr1
> 100001-100100.
>
> Is this possible?
>
> I hope I was clear...
>
> Thank you ,
> David
>
>
------------------------------------------------------------------------
> ------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: GFF question

Scott Cain
Hi David,

I agree with Pushkala that it is generally not possible with GFF
adaptors (Bio::DB::GFF and Bio::DB::SeqFeature::Store).  It is
theoretically possible with the Chado adaptor, but at the expense of
both work on your part and rendering time in GBrowse.  There is an
option for the Bio::DB::Das::Chado adaptor called recursivMapping.
The pod description for it is below, though I must admit, I haven't
tested this option in a long time (years).

       -recursivMapping [1|0] default: 0
           In the case where features are mapped to a "small" srcfeature (like
           a contig) and then that small feature is mapped to a larger feature
           (like a chromosome), setting -recursivMapping will allow the Chado
           adaptor to calculate the coordinates of the feature on the larger
           feature even though it isn't explicitly mapped to it.  The Chado
           adaptor suffers an approximately 20% performance penalty to do this
           mapping.

Scott



On Thu, Jul 8, 2010 at 3:08 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Aah! No. That you wouldn't be able to do..
> Although, one may be able to show that in an "init_code" ... just may
> be.. im sure people on the forum will have something interesting to say
> about this..
>
> Although, the glyphs also have a feature wherein you can activate "box
> subparts" so mousing over a part of the gene which has an exon, will
> show you coordinates for that exon (relative to the chromosome, not the
> gene) in that gene. The search tab will also be able to search for exons
> coordinates (relative to the chromosome) instead of gene coordinates..
> given that your gff3 file has it..
> Gbrowse2 SeqFeature Store allows users that depth in storage..but Im
> sure, coordinates relative to gene is doable in the init_code of the
> data source conf file.. never tried it though..
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: David Breimann [mailto:[hidden email]]
> Sent: Thursday, July 08, 2010 1:59 PM
> To: Jayaraman, Pushkala
> Subject: Re: [Gmod-gbrowse] GFF question
>
> I'm not sure I understand you...
> Maybe a good example will be a chromosome and a gene within it.
> I have a GFF for some chromosome listing all the genes within it.
> Can I use features with coordinate relative to some specific gene?
> (e.g. introns/exons with positions relative to the gene start instead
> of absolute positions in the chromosome).
>
> On Thu, Jul 8, 2010 at 9:14 PM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>> Are you trying to ask whether you can visualize a region within a
>> chromosome while having features on the chromosome as well..
>> :)
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: David Breimann [mailto:[hidden email]]
>> Sent: Thursday, July 08, 2010 12:33 PM
>> To: [hidden email]
>> Subject: [Gmod-gbrowse] GFF question
>>
>> I'm trying to figure out how to use relative coordinates in a GFF file
>> under GBrowse.
>>
>> Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
>> its sequence and annotations into GBrowse.
>>
>> Now I would like to focus (mentally... not visually :)) on a specific
>> region within this chromosome ("region1") of 100kb - let's say
>> chr1:100001-200000, and use a GFF file
>> (region1.gff) with coordinate relative to region1, e.g. a feature in
>> region.gff with coordinates 1 100 will be displayed on chr1
>> 100001-100100.
>>
>> Is this possible?
>>
>> I hope I was clear...
>>
>> Thank you ,
>> David
>>
>>
> ------------------------------------------------------------------------
>> ------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
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>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GFF question

David Breimann
OK, I guess I will work around that. Thank you Pushkala and Scott!

On Thu, Jul 8, 2010 at 10:18 PM, Scott Cain <[hidden email]> wrote:

> Hi David,
>
> I agree with Pushkala that it is generally not possible with GFF
> adaptors (Bio::DB::GFF and Bio::DB::SeqFeature::Store).  It is
> theoretically possible with the Chado adaptor, but at the expense of
> both work on your part and rendering time in GBrowse.  There is an
> option for the Bio::DB::Das::Chado adaptor called recursivMapping.
> The pod description for it is below, though I must admit, I haven't
> tested this option in a long time (years).
>
>       -recursivMapping [1|0] default: 0
>           In the case where features are mapped to a "small" srcfeature (like
>           a contig) and then that small feature is mapped to a larger feature
>           (like a chromosome), setting -recursivMapping will allow the Chado
>           adaptor to calculate the coordinates of the feature on the larger
>           feature even though it isn't explicitly mapped to it.  The Chado
>           adaptor suffers an approximately 20% performance penalty to do this
>           mapping.
>
> Scott
>
>
>
> On Thu, Jul 8, 2010 at 3:08 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Aah! No. That you wouldn't be able to do..
>> Although, one may be able to show that in an "init_code" ... just may
>> be.. im sure people on the forum will have something interesting to say
>> about this..
>>
>> Although, the glyphs also have a feature wherein you can activate "box
>> subparts" so mousing over a part of the gene which has an exon, will
>> show you coordinates for that exon (relative to the chromosome, not the
>> gene) in that gene. The search tab will also be able to search for exons
>> coordinates (relative to the chromosome) instead of gene coordinates..
>> given that your gff3 file has it..
>> Gbrowse2 SeqFeature Store allows users that depth in storage..but Im
>> sure, coordinates relative to gene is doable in the init_code of the
>> data source conf file.. never tried it though..
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: David Breimann [mailto:[hidden email]]
>> Sent: Thursday, July 08, 2010 1:59 PM
>> To: Jayaraman, Pushkala
>> Subject: Re: [Gmod-gbrowse] GFF question
>>
>> I'm not sure I understand you...
>> Maybe a good example will be a chromosome and a gene within it.
>> I have a GFF for some chromosome listing all the genes within it.
>> Can I use features with coordinate relative to some specific gene?
>> (e.g. introns/exons with positions relative to the gene start instead
>> of absolute positions in the chromosome).
>>
>> On Thu, Jul 8, 2010 at 9:14 PM, Jayaraman, Pushkala <[hidden email]>
>> wrote:
>>> Are you trying to ask whether you can visualize a region within a
>>> chromosome while having features on the chromosome as well..
>>> :)
>>>
>>> Pushkala Jayaraman
>>> Programmer/Analyst
>>> Rat Genome Database
>>> Human and Molecular Genetics Center
>>> Medical College of Wisconsin
>>> Email: [hidden email]
>>> Work: 414-955-2229
>>> www.rgd.mcw.edu
>>>
>>>
>>> -----Original Message-----
>>> From: David Breimann [mailto:[hidden email]]
>>> Sent: Thursday, July 08, 2010 12:33 PM
>>> To: [hidden email]
>>> Subject: [Gmod-gbrowse] GFF question
>>>
>>> I'm trying to figure out how to use relative coordinates in a GFF file
>>> under GBrowse.
>>>
>>> Let's say I have I have a chromosome ("chr1") of size 5Mbp. I loaded
>>> its sequence and annotations into GBrowse.
>>>
>>> Now I would like to focus (mentally... not visually :)) on a specific
>>> region within this chromosome ("region1") of 100kb - let's say
>>> chr1:100001-200000, and use a GFF file
>>> (region1.gff) with coordinate relative to region1, e.g. a feature in
>>> region.gff with coordinates 1 100 will be displayed on chr1
>>> 100001-100100.
>>>
>>> Is this possible?
>>>
>>> I hope I was clear...
>>>
>>> Thank you ,
>>> David
>>>
>>>
>> ------------------------------------------------------------------------
>>> ------
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

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