ncRNA GFF3 export issue

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ncRNA GFF3 export issue

Erika Sallet-2

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line.

Example of a ncRNA from the first group:

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika

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Re: ncRNA GFF3 export issue

nathandunn

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <[hidden email]> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line.

Example of a ncRNA from the first group:

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


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Re: ncRNA GFF3 export issue

Erika Sallet-2
- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

apollo_win.png



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="zrPmQ8QsDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">esa...@...> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line.

Example of a ncRNA from the first group:

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


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Re: ncRNA GFF3 export issue

nathandunn

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:


And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    [hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    [hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    [hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    [hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

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Re: ncRNA GFF3 export issue

Erika Sallet-2

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:

<a href="https://www.google.com/url?q=https%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Demo.html

And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="zvBWz2mCDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">esa...@...> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    <a href="javascript:" target="_blank" gdf-obfuscated-mailto="zvBWz2mCDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">owner=er...@inra.fr;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    <a href="javascript:" target="_blank" gdf-obfuscated-mailto="zvBWz2mCDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">owner=er...@inra.fr;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    <a href="javascript:" target="_blank" gdf-obfuscated-mailto="zvBWz2mCDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">owner=er...@inra.fr;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    <a href="javascript:" target="_blank" gdf-obfuscated-mailto="zvBWz2mCDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">owner=er...@inra.fr;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@<a href="http://gmail.com/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://gmail.com/&#39;;return true;" onclick="this.href=&#39;http://gmail.com/&#39;;return true;">gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

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Re: ncRNA GFF3 export issue

Erika Sallet-2
Hi,

I cannot create a new annotation in the user track with the demo server. I use the human genome Hg38. Is this normal?
 When I load the page on Chrome, I get this message on the console:

console.png



Thank for your help
Erika

Le lundi 20 janvier 2020 11:07:02 UTC+1, Erika Sallet a écrit :

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:

<a href="https://www.google.com/url?q=https%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Demo.html

And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@<a href="http://gmail.com/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://gmail.com/&#39;;return true;" onclick="this.href=&#39;http://gmail.com/&#39;;return true;">gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

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Re: ncRNA GFF3 export issue

nathandunn

Erika,

No, that is not normal.   

Can you try an incognito window within Chrome or a different browser? 

Also, my version of Chrome is "Version 79.0.3945.117 (Official Build) (64-bit)" on a Mac

Is yours up to date or is there a proxy issue with your client? 

Mine looks like this:


Thanks,

Nathan


On Jan 21, 2020, at 4:03 AM, Erika Sallet <[hidden email]> wrote:

Hi,

I cannot create a new annotation in the user track with the demo server. I use the human genome Hg38. Is this normal?
 When I load the page on Chrome, I get this message on the console:

<console.png>



Thank for your help
Erika

Le lundi 20 janvier 2020 11:07:02 UTC+1, Erika Sallet a écrit :

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:


And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

<console.png>

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Re: ncRNA GFF3 export issue

Erika Sallet-2
It works with Firefox version 68.2.0. Thanks

In the demo server, I loaded a new track from this GFF3:
##gff-version 3
chr2    .    gene    11300    19000    .    +    .    ID=ncRNA1;Name=test
chr2    .    ncRNA    11300    19000    .    +    .    ID=ncRNA1.1;Parent=ncRNA1
chr2    .    gene    110000    112000    .    +    .    ID=ncRNA2;Name=ncRNA2
chr2    .    ncRNA    110000    112000    .    +    .    ID=ncRNA2.1;Parent=ncRNA2

Then I created two new ncRNAs in the User tracks, ncRNA1.1 and ncRNA2.1. There are visible in the Annotation panel. 
I still can't export them by clicking on the button "Save TrackData/GFF3/Only GFF3"
Do you have any ideas for solving this problem?

Erika


Le mardi 21 janvier 2020 20:32:02 UTC+1, Nathan Dunn a écrit :

Erika,

No, that is not normal.   

Can you try an incognito window within Chrome or a different browser? 

Also, my version of Chrome is "Version 79.0.3945.117 (Official Build) (64-bit)" on a Mac

Is yours up to date or is there a proxy issue with your client? 

Mine looks like this:


Thanks,

Nathan


On Jan 21, 2020, at 4:03 AM, Erika Sallet <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="7U1RElxyDgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">esa...@...> wrote:

Hi,

I cannot create a new annotation in the user track with the demo server. I use the human genome Hg38. Is this normal?
 When I load the page on Chrome, I get this message on the console:

<console.png>



Thank for your help
Erika

Le lundi 20 janvier 2020 11:07:02 UTC+1, Erika Sallet a écrit :

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:

<a href="https://www.google.com/url?q=https%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Demo.html

And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@<a href="http://gmail.com/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://gmail.com/&#39;;return true;" onclick="this.href=&#39;http://gmail.com/&#39;;return true;">gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

<console.png>

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Re: ncRNA GFF3 export issue

nathandunn

It looks like you found a bug where we don’t export genes if they lack an exon. 

I’m assuming in this case, an exon would be inappropriate.  

I’ve added an issue and will try to get this fixed:  https://github.com/GMOD/Apollo/issues/2353

If you don’t have a lot, you can just right-click and export individual annotations, otherwise you might be better off creating a fake exon initially and then peeling it away at the end (ugh).  Hopefully I can get to this sooner than later though. 

Nathan


On Jan 22, 2020, at 12:24 AM, Erika Sallet <[hidden email]> wrote:

It works with Firefox version 68.2.0. Thanks

In the demo server, I loaded a new track from this GFF3:
##gff-version 3
chr2    .    gene    11300    19000    .    +    .    ID=ncRNA1;Name=test
chr2    .    ncRNA    11300    19000    .    +    .    ID=ncRNA1.1;Parent=ncRNA1
chr2    .    gene    110000    112000    .    +    .    ID=ncRNA2;Name=ncRNA2
chr2    .    ncRNA    110000    112000    .    +    .    ID=ncRNA2.1;Parent=ncRNA2

Then I created two new ncRNAs in the User tracks, ncRNA1.1 and ncRNA2.1. There are visible in the Annotation panel. 
I still can't export them by clicking on the button "Save TrackData/GFF3/Only GFF3"
Do you have any ideas for solving this problem?

Erika


Le mardi 21 janvier 2020 20:32:02 UTC+1, Nathan Dunn a écrit :

Erika,

No, that is not normal.   

Can you try an incognito window within Chrome or a different browser? 

Also, my version of Chrome is "Version 79.0.3945.117 (Official Build) (64-bit)" on a Mac

Is yours up to date or is there a proxy issue with your client? 

Mine looks like this:


Thanks,

Nathan


On Jan 21, 2020, at 4:03 AM, Erika Sallet <[hidden email]> wrote:

Hi,

I cannot create a new annotation in the user track with the demo server. I use the human genome Hg38. Is this normal?
 When I load the page on Chrome, I get this message on the console:

<console.png>



Thank for your help
Erika

Le lundi 20 janvier 2020 11:07:02 UTC+1, Erika Sallet a écrit :

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:


And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


<apollo_win.png>

<console.png>


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Re: ncRNA GFF3 export issue

nathandunn
Erika,

This should be fixed on the development branch now as well as the latest docker.  

Please test me know if it fixes it or not when you have time.  

Thanks,

Nathan


On Wednesday, January 22, 2020 at 4:55:29 PM UTC-8, Nathan Dunn wrote:

It looks like you found a bug where we don’t export genes if they lack an exon. 

I’m assuming in this case, an exon would be inappropriate.  

I’ve added an issue and will try to get this fixed:  <a href="https://github.com/GMOD/Apollo/issues/2353" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2353\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFVHfbgDyCNG_dV3G0CRpSKN5Gqw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2353\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFVHfbgDyCNG_dV3G0CRpSKN5Gqw&#39;;return true;">https://github.com/GMOD/Apollo/issues/2353

If you don’t have a lot, you can just right-click and export individual annotations, otherwise you might be better off creating a fake exon initially and then peeling it away at the end (ugh).  Hopefully I can get to this sooner than later though. 

Nathan


On Jan 22, 2020, at 12:24 AM, Erika Sallet <[hidden email]> wrote:

It works with Firefox version 68.2.0. Thanks

In the demo server, I loaded a new track from this GFF3:
##gff-version 3
chr2    .    gene    11300    19000    .    +    .    ID=ncRNA1;Name=test
chr2    .    ncRNA    11300    19000    .    +    .    ID=ncRNA1.1;Parent=ncRNA1
chr2    .    gene    110000    112000    .    +    .    ID=ncRNA2;Name=ncRNA2
chr2    .    ncRNA    110000    112000    .    +    .    ID=ncRNA2.1;Parent=ncRNA2

Then I created two new ncRNAs in the User tracks, ncRNA1.1 and ncRNA2.1. There are visible in the Annotation panel. 
I still can't export them by clicking on the button "Save TrackData/GFF3/Only GFF3"
Do you have any ideas for solving this problem?

Erika


Le mardi 21 janvier 2020 20:32:02 UTC+1, Nathan Dunn a écrit :

Erika,

No, that is not normal.   

Can you try an incognito window within Chrome or a different browser? 

Also, my version of Chrome is "Version 79.0.3945.117 (Official Build) (64-bit)" on a Mac

Is yours up to date or is there a proxy issue with your client? 

Mine looks like this:


Thanks,

Nathan


On Jan 21, 2020, at 4:03 AM, Erika Sallet <[hidden email]> wrote:

Hi,

I cannot create a new annotation in the user track with the demo server. I use the human genome Hg38. Is this normal?
 When I load the page on Chrome, I get this message on the console:

<console.png>



Thank for your help
Erika

Le lundi 20 janvier 2020 11:07:02 UTC+1, Erika Sallet a écrit :

Here are the details of the evidence (EGNPP-3-20180829)


###
RSc    EuGene    gene    5142    5167    .    -    .    ID=gene:SMALLRSc.13;Name=RSc5005;locus_tag=RSc5005;source=smallRNA_library
RSc    EuGene    ncRNA    5142    5167    .    -    .    ID=ncRNA:SMALLRSc.13;Name=RSc5005;Parent=gene:SMALLRSc.13;locus_tag=RSc5005;source=smallRNA_library
###

###
RSc    EuGene    gene    6117    6151    .    +    .    ID=gene:SMALLRSc.18;Name=RSc5006;locus_tag=RSc5006;source=smallRNA_library
RSc    EuGene    ncRNA    6117    6151    .    +    .    ID=ncRNA:SMALLRSc.18;Name=RSc5006;Parent=gene:SMALLRSc.18;locus_tag=RSc5006;source=smallRNA_library
###



When the user creates a manual annotation in this way "right click/Create new annotation/new ncRNA", there is no exon in the new ncRNA. When the user drags the ncRNA into the "User created annotation" track, then changes the annotation type to ncRNA (he must do so because the created feature is at that time a coding gene) , there is an exon.



OK, I will test the 2.5.0 version with your demo server and see the gff3 export behaviour.

Erika


Le samedi 18 janvier 2020 19:14:59 UTC+1, Nathan Dunn a écrit :

What are the details of the evidence (GFF or screenshot)?

Oh, if you are using Apollo 2.1.0 I think that upgrading to the most recent stable version (2.5.0) should fix this. But let me know if I’m misconstrued your versioning.  

If you want to test it on 2.5.0 we have instructions for using our demo site here in order to replicate what you are doing:

<a href="https://www.google.com/url?q=https%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Demo.html

And just to clarify, we won’t support exporting a transcript without an associated gene or pseudogene.  At least not at this time.  

Hope t his helps

Nathan


On Jan 18, 2020, at 6:32 AM, Erika Sallet <[hidden email]> wrote:

- Are you creating an isoform in this case?
No.

- Can you provide a screenshot of the relevant areas?
In this area, RSc5005a-00001 is not present in the generated global GFF3 file, while RSc5006a-00001 is present.

<apollo_win.png>



- What version of Apollo are you using?
apollo_2.10

- Why you are disassociating the ncRNA from the gene in this case?
We want  to manage  the original ncRNAs (coming from the track EGNPP-3-20180829) separately from the new manually annotated ncRNA, and consider them as two different objects.

I add the corresponding GFF3 outputs after a right click on each ncRNA:

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    5142    5167    .    -    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=RSc5005a;date_creation=2019-07-05
RSc    .    ncRNA    5142    5167    .    -    .    owner=[hidden email];Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=RSc5005a-00001;status=Validated;date_creation=2019-07-05
###

##gff-version 3
##sequence-region RSc 1 3716413
RSc    .    gene    6117    6151    .    +    .    owner=[hidden email];Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=RSc5006a;date_creation=2019-07-05
RSc    .    ncRNA    6117    6151    .    +    .    owner=[hidden email];Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=RSc5006a-00001;status=Validated;date_creation=2019-07-05
RSc    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###

Thanks

Best regards
Erika

Le vendredi 17 janvier 2020 17:05:29 UTC+1, Nathan Dunn a écrit :

I’m not seeing this yet when trying both ways of creating the model, but hopefully we can figure out why.  

I have a few follow-up questions:

- Are you creating an isoform in this case?
- Can you provide a screenshot of the relevant areas?
- What version of Apollo are you using?
- Why you are disassociating the ncRNA from the gene in this case?

Nathan


On Jan 17, 2020, at 12:26 AM, Erika Sallet <esa...@<a href="http://gmail.com/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://gmail.com/&#39;;return true;" onclick="this.href=&#39;http://gmail.com/&#39;;return true;">gmail.com> wrote:

Hello,


I get a problem during the GFF3 export of ncRNAs. I have two types of ncRNAs in the User-created annotation track:

-The first group was created with these actions: Add transcript + Change annotation type + Dissociated transcript from gene

-The second group with: Add feature  + Dissociated transcript from gene


When I try to export in GFF3 with "Save TrackData/GFF3/Only GFF3" button, only the ncRNAs from the first group are exported. I get the same result using the get_gff3.groovy script.


When I directly generate individual GFF3  with a right click on the ncRNA, I notice a difference: the ncRNAs of the second group have no exon line. 

Example of a ncRNA from the first group: 

##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    6117    6151    .    +    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=aa52b45b-9133-491a-9220-0328c04523bd;date_last_modified=2019-07-05;Name=Chr15006a;date_creation=2019-07-05
Chr1    .    ncRNA    6117    6151    .    +    .    owner=XXXX@XXX;Parent=aa52b45b-9133-491a-9220-0328c04523bd;Note=Manually dissociate transcript from gene;ID=888c249d-262e-47a8-a207-820c3f4eb5ba;date_last_modified=2019-07-05;Name=Chr15006a-00001;status=Validated;date_creation=2019-07-05
Chr1    .    exon    6117    6151    .    +    .    Parent=888c249d-262e-47a8-a207-820c3f4eb5ba;ID=06a3353d-b898-466a-a393-27aecaa99186;Name=06a3353d-b898-466a-a393-27aecaa99186
###


Example from the second group:


##gff-version 3
##sequence-region Chr1 1 3716413
Chr1    .    gene    5142    5167    .    -    .    owner=
XXXX@XXX;Note=Manually dissociate transcript from gene;ID=913d592d-12cb-4502-8520-5897aed20acd;date_last_modified=2019-07-05;Name=Chr15005a;date_creation=2019-07-05
Chr1    .    ncRNA    5142    5167    .    -    .    owner=
XXXX@XXX;Parent=913d592d-12cb-4502-8520-5897aed20acd;Note=Manually dissociate transcript from gene;ID=9ebfe3ad-5cca-44b0-8727-07ad4637de43;date_last_modified=2019-07-05;Name=Chr15005a-00001;status=Validated;date_creation=2019-07-05
###


The annotators generated a lot of data in the User-created annotation track so I would need the global GFF3 export functionality.

Can you help me solve that problem? thank you in advance!

Best regard


Erika


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