CDS and exon segments

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CDS and exon segments

Vaneet Lotay

Hello all,

 

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

 

Thanks,

 

Vaneet


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Re: CDS and exon segments

Alexey Morozov
Well, mRNAs, CDS'es and exons are separate tracks and AFAIK their parent-child relationships are irrelevant. Unless, of course, you ask for them explicitly in some sub of your own.
So the difference in segment positions is because they are different in your data (probably stop codons removed from CDSes for a lack of aminoacid or something). If you don't like it - edit your GFFs.

2015-02-24 6:02 GMT+08:00 Vaneet Lotay <[hidden email]>:

Hello all,

 

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

 

Thanks,

 

Vaneet


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Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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Re: CDS and exon segments

Vaneet Lotay

Thanks for responding Alexey.  I realized they have different start/stop positions in my data, that’s not my issue.  I’m not concerned why that occurs in the data file, I’m more curious as how GBrowse compiles the GFF3 files when it sees both CDSs and exons within an mRNA.  Which one does it decide to draw?  I was expecting them to see both of them drawn but it looks like it only draws one of them perhaps the CDSs.  Because if I remove the CDSs and just keep the exons it just draws one solid block for the mRNA so then you lose information in the track drawing which is no good.  However I believe in the past we’ve loaded ‘only  exon’ files and they’ve visually looked fine.  So maybe there’s something I’m missing when it comes to what GBrowse looks for when it goes through your GFF3 file line by line?

 

Obviously if the CDSs and exons perfectly overlap which has been the case sometimes in the past you won’t be able to tell if it’s drawing them both.

 

Vaneet

 

From: Alexey Morozov [mailto:[hidden email]]
Sent: Wednesday, February 25, 2015 8:46 AM
To: Vaneet Lotay
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] CDS and exon segments

 

Well, mRNAs, CDS'es and exons are separate tracks and AFAIK their parent-child relationships are irrelevant. Unless, of course, you ask for them explicitly in some sub of your own.

So the difference in segment positions is because they are different in your data (probably stop codons removed from CDSes for a lack of aminoacid or something). If you don't like it - edit your GFFs.

 

2015-02-24 6:02 GMT+08:00 Vaneet Lotay <[hidden email]>:

Hello all,

 

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

 

Thanks,

 

Vaneet


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Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


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Re: CDS and exon segments

Alexey Morozov
It decides to draw whatever tracks are declared in your_genome.conf file. From what you say, it's probably CDSes and mRNA. See http://gmod.org/wiki/GBrowse_2.0_HOWTO#Track_Definitions for howto on gbrowse configuration.

2015-02-26 2:13 GMT+08:00 Vaneet Lotay <[hidden email]>:

Thanks for responding Alexey.  I realized they have different start/stop positions in my data, that’s not my issue.  I’m not concerned why that occurs in the data file, I’m more curious as how GBrowse compiles the GFF3 files when it sees both CDSs and exons within an mRNA.  Which one does it decide to draw?  I was expecting them to see both of them drawn but it looks like it only draws one of them perhaps the CDSs.  Because if I remove the CDSs and just keep the exons it just draws one solid block for the mRNA so then you lose information in the track drawing which is no good.  However I believe in the past we’ve loaded ‘only  exon’ files and they’ve visually looked fine.  So maybe there’s something I’m missing when it comes to what GBrowse looks for when it goes through your GFF3 file line by line?

 

Obviously if the CDSs and exons perfectly overlap which has been the case sometimes in the past you won’t be able to tell if it’s drawing them both.

 

Vaneet

 

From: Alexey Morozov [mailto:[hidden email]]
Sent: Wednesday, February 25, 2015 8:46 AM
To: Vaneet Lotay
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] CDS and exon segments

 

Well, mRNAs, CDS'es and exons are separate tracks and AFAIK their parent-child relationships are irrelevant. Unless, of course, you ask for them explicitly in some sub of your own.

So the difference in segment positions is because they are different in your data (probably stop codons removed from CDSes for a lack of aminoacid or something). If you don't like it - edit your GFFs.

 

2015-02-24 6:02 GMT+08:00 Vaneet Lotay <[hidden email]>:

Hello all,

 

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

 

Thanks,

 

Vaneet


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--

Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.




--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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Re: CDS and exon segments

Timothy Parnell
In reply to this post by Vaneet Lotay
It depends on the glyph that is being used, which is defined in the track stanza in your conf file. Take a look at the documentation for Bio::Graphics::gene, Bio::Graphics::processed_transcript, and Bio::Graphics::segment as starting points. For most of these, it assumes proper parent-child relationships are defined in the GFF3 file based on the Sequence Ontology GFF3 specification. Some subfeature types are preferred, others used as a fallback, and still others ignored.


On Feb 25, 2015, at 11:13 AM, Vaneet Lotay <[hidden email]<mailto:[hidden email]>> wrote:

Thanks for responding Alexey.  I realized they have different start/stop positions in my data, that’s not my issue.  I’m not concerned why that occurs in the data file, I’m more curious as how GBrowse compiles the GFF3 files when it sees both CDSs and exons within an mRNA.  Which one does it decide to draw?  I was expecting them to see both of them drawn but it looks like it only draws one of them perhaps the CDSs.  Because if I remove the CDSs and just keep the exons it just draws one solid block for the mRNA so then you lose information in the track drawing which is no good.  However I believe in the past we’ve loaded ‘only  exon’ files and they’ve visually looked fine.  So maybe there’s something I’m missing when it comes to what GBrowse looks for when it goes through your GFF3 file line by line?

Obviously if the CDSs and exons perfectly overlap which has been the case sometimes in the past you won’t be able to tell if it’s drawing them both.

Vaneet

From: Alexey Morozov [mailto:[hidden email]]
Sent: Wednesday, February 25, 2015 8:46 AM
To: Vaneet Lotay
Cc: [hidden email]<mailto:[hidden email]>
Subject: Re: [Gmod-gbrowse] CDS and exon segments

Well, mRNAs, CDS'es and exons are separate tracks and AFAIK their parent-child relationships are irrelevant. Unless, of course, you ask for them explicitly in some sub of your own.
So the difference in segment positions is because they are different in your data (probably stop codons removed from CDSes for a lack of aminoacid or something). If you don't like it - edit your GFFs.

2015-02-24 6:02 GMT+08:00 Vaneet Lotay <[hidden email]<mailto:[hidden email]>>:
Hello all,

Lately I’ve been getting a lot of GFF3 files with both CDS and exon segments linked to each mRNA segment with a child-parent relationship.  The only thing is sometimes but not every time the CDS segments will not perfectly overlap with the stop positions of the mRNA and the matching exons.  Usually the last exon does perfectly overlap with the end of the mRNA from what I’ve found.  What I’m curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesn’t draw both CDS and exons.  Does it only look for one of the keywords?  If you removed all CDS segments would it still draw the mRNA in exon/intron transcript style?

Thanks,

Vaneet

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--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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