[Gmod-gbrowse] CDS and exon segments

Discussion:

Vaneet Lotay

2015-02-23 22:02:31 UTC

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

Alexey Morozov

2015-02-25 15:46:04 UTC

Permalink

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.

Post by Vaneet Lotay
Hello all,
Lately Iâve 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 Iâve found. What Iâm curious is how GBrowse compiles or
reads these GFF3 files with both these segments because clearly it doesnât
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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Vaneet Lotay

2015-02-25 18:13:41 UTC

Permalink

Thanks for responding Alexey. I realized they have different start/stop positions in my data, thatâs not my issue. Iâm not concerned why that occurs in the data file, Iâm 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 weâve loaded âonly exonâ files and theyâve visually looked fine. So maybe thereâs something Iâm 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 wonât be able to tell if itâs drawing them both.

Vaneet

From: Alexey Morozov [mailto:***@gmail.com]
Sent: Wednesday, February 25, 2015 8:46 AM
To: Vaneet Lotay
Cc: gmod-***@lists.sourceforge.net
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 <***@ucalgary.ca<mailto:***@ucalgary.ca>>:
Hello all,

Lately Iâve 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 Iâve found. What Iâm curious is how GBrowse compiles or reads these GFF3 files with both these segments because clearly it doesnât 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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LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

Alexey Morozov

2015-02-26 03:15:24 UTC

Permalink

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.

Thanks for responding Alexey. I realized they have different start/stop
positions in my data, thatâs not my issue. Iâm not concerned why that
occurs in the data file, Iâm 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 weâve loaded âonly exonâ files and theyâve
visually looked fine. So maybe thereâs something Iâm 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 wonât be able to tell if itâs drawing them both.
Vaneet
*Sent:* Wednesday, February 25, 2015 8:46 AM
*To:* Vaneet Lotay
*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.
Hello all,
Lately Iâve 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 Iâve found. What Iâm curious is how GBrowse compiles or
reads these GFF3 files with both these segments because clearly it doesnât
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.

Timothy Parnell

2015-02-26 16:32:23 UTC

Permalink

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 <***@ucalgary.ca<mailto:***@ucalgary.ca>> 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:***@gmail.com]
Sent: Wednesday, February 25, 2015 8:46 AM
To: Vaneet Lotay
Cc: gmod-***@lists.sourceforge.net<mailto:gmod-***@lists.sourceforge.net>
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 <***@ucalgary.ca<mailto:***@ucalgary.ca>>:
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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