apollo canvas features

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apollo canvas features

Prashant S Hosmani
Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA







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Re: apollo canvas features

nathandunn

Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: apollo canvas features

Prashant S Hosmani
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 

And for this gff looks like this-


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 


If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: apollo canvas features

Deepak Unni
Hi Prashant,

Could you share the command that you used while processing your GFF3 with flatfile-to-json.pl ?


Thanks,

Deepak



On Mon, Feb 13, 2017 at 11:11 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 

And for this gff looks like this-


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 


If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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Re: apollo canvas features

Prashant S Hosmani
Hi Deepak,

Here is the command which I use with sudo access

flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --trackLabel “gene models"

Thanks you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:27 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Could you share the command that you used while processing your GFF3 with flatfile-to-json.pl ?


Thanks,

Deepak



On Mon, Feb 13, 2017 at 11:11 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 
<PastedGraphic-3.png>

And for this gff looks like this-
<PastedGraphic-4.png>


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 

<PastedGraphic-2.png>

If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: apollo canvas features

Deepak Unni
Hi Prashant,

Thanks for the command. 

So it looks like when you are creating a track via flatfile-to-json.pl, the script (by default) treats gene as the top level feature instead of mRNA. We recommend that you specify, explicitly, what the top level feature should be.

When you 'Create a new Annotation', even though the CanvasFeatures track renders the gene model properly, what is provided to Apollo is still the gene span.

I would suggest try running flatfile-to-json.pl again, but this time with an additional argument --type,

Ex:
flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --type mRNA --trackLabel “gene models"


Cheers,

Deepak

On Mon, Feb 13, 2017 at 11:32 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Deepak,

Here is the command which I use with sudo access

flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --trackLabel “gene models"

Thanks you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:27 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Could you share the command that you used while processing your GFF3 with flatfile-to-json.pl ?


Thanks,

Deepak



On Mon, Feb 13, 2017 at 11:11 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 
<PastedGraphic-3.png>

And for this gff looks like this-
<PastedGraphic-4.png>


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 

<PastedGraphic-2.png>

If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: apollo canvas features

Prashant S Hosmani
Hi Deepak.

Thank you for the fix. With specifying —type mRNA while creating track, I can right click the gene model renders a proper gene model with exon features. This is great start.

Another issue is that I cannot select that gene model as it open a details of gene model. So I cannot drag this gene model to apollo track (and also loses highlighting ability). Is there a way to disable onclick behavior of this track?

Thank you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:40 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Thanks for the command. 

So it looks like when you are creating a track via flatfile-to-json.pl, the script (by default) treats gene as the top level feature instead of mRNA. We recommend that you specify, explicitly, what the top level feature should be.

When you 'Create a new Annotation', even though the CanvasFeatures track renders the gene model properly, what is provided to Apollo is still the gene span.

I would suggest try running flatfile-to-json.pl again, but this time with an additional argument --type,

Ex:
flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --type mRNA --trackLabel “gene models"


Cheers,

Deepak

On Mon, Feb 13, 2017 at 11:32 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Deepak,

Here is the command which I use with sudo access

flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --trackLabel “gene models"

Thanks you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:27 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Could you share the command that you used while processing your GFF3 with flatfile-to-json.pl ?


Thanks,

Deepak



On Mon, Feb 13, 2017 at 11:11 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 
<PastedGraphic-3.png>

And for this gff looks like this-
<PastedGraphic-4.png>


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 

<PastedGraphic-2.png>

If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






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University of Missouri, Columbia



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S104A Animal Science Research Center,
University of Missouri, Columbia



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Re: apollo canvas features

Deepak Unni
Hi Prashant,

Glad to hear that it worked out.

As for the issue with not being able to drag gene models - This is a limitation of the CanvasFeatures track where there is no click, double-click, and drag behavior for features represented on the track. Although there has been a lot of discussion on how to add this ability, there is no immediate solution at this time. 

For the purpose at hand, I would recommend preferring HTMLFeatures over CanvasFeatures to retain drag-behavior.

Cheers,

Deepak


On Mon, Feb 13, 2017 at 11:50 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Deepak.

Thank you for the fix. With specifying —type mRNA while creating track, I can right click the gene model renders a proper gene model with exon features. This is great start.

Another issue is that I cannot select that gene model as it open a details of gene model. So I cannot drag this gene model to apollo track (and also loses highlighting ability). Is there a way to disable onclick behavior of this track?

Thank you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:40 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Thanks for the command. 

So it looks like when you are creating a track via flatfile-to-json.pl, the script (by default) treats gene as the top level feature instead of mRNA. We recommend that you specify, explicitly, what the top level feature should be.

When you 'Create a new Annotation', even though the CanvasFeatures track renders the gene model properly, what is provided to Apollo is still the gene span.

I would suggest try running flatfile-to-json.pl again, but this time with an additional argument --type,

Ex:
flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --type mRNA --trackLabel “gene models"


Cheers,

Deepak

On Mon, Feb 13, 2017 at 11:32 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Deepak,

Here is the command which I use with sudo access

flatfile-to-json.pl --gff gene_models.gff --out . --tracktype "CanvasFeatures" --trackLabel “gene models"

Thanks you,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 12:27 PM, Deepak Unni <[hidden email]> wrote:

Hi Prashant,

Could you share the command that you used while processing your GFF3 with flatfile-to-json.pl ?


Thanks,

Deepak



On Mon, Feb 13, 2017 at 11:11 AM, Prashant S Hosmani <[hidden email]> wrote:
Hi Nathan,

Thank you for you response. Here are more details with screenshots.

If right click on gff track for gene model and create new annotation, this is how it looks. It basically creates a gene span. 
<PastedGraphic-3.png>

And for this gff looks like this-
<PastedGraphic-4.png>


Here is another track - transcript. If I drag up Featuretrack for transcript it shows properly. And its gff has match and match part rather than gene models with exons. 

<PastedGraphic-2.png>

If I make this track as CanvasFeatures, it becomes one big exon with transcript span (Without exon structure).


1 - what plugins do you have installed? 
I have not installed any plug-ins other than the default configuration. Do I need any plug-ins to enable CanvasFeatures?

2 - what is your configuration for the track in the trackList.json? 
Here is config for gene models
      {
         "key" : "gene models",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/gene models/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Gene Models",
         "label" : "gene models",
         "type" : "CanvasFeatures"
      },



Thank you and any input will be much appreciated.
Prashant

Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



On Feb 13, 2017, at 11:45 AM, Nathan Dunn <[hidden email]> wrote:


Prashant,

Everything you have said is correct, but it sounds like there might be a problem in your data or configuration somewhere somewhere. 

When you drag up the transcript from the FeatureTrack / DraggableHTMLFeatures track does it render all of the exons correctly manual annotation space? 

Quick question:

1 - what plugins do you have installed? 
2 - what is your configuration for the track in the trackList.json? 
3 - any screenshots or GFF3 would be helpful.  

Thanks,

Nathan

On Feb 12, 2017, at 11:52 AM, Prashant S Hosmani <[hidden email]> wrote:

Dear All,

I’m using Apollo 2.0.5 for few of the genomes. I have various tracks and one of the important track is the gene models. I’m using CanvasFeatures and tracks gets displayed properly. But these tracks are not apollo friendly. Cannot drag these gene models and if I create gene model for editing using right click it creates a gene span in apollo track. It may also be that mouse over and left click features of CanvasFeatures are blocking dragging capability in apollo.

With FeatureTrack, gene models track become drag friendly but it doesn’t  show exon structures of gene models. 

In apollo, FeatureTrack become DraggableHTMLFeatures and CanvasFeatures become WebApolloCanvasFeatures in apollo.

Is there a apollo recommended json settings for gene models? Let me know If I need to change apollo config groovy settings.

Thanks,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



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--
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S104A Animal Science Research Center,
University of Missouri, Columbia




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