trackable tracks / conversion

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trackable tracks / conversion

Michael Paulini
Hia,

I was looking for a way to prevent webapollo from converting tracks that
are dragged into the curation area to CDSes and rather specify a biotype
for them, so ncRNA tracks or genome features stay the type they are.

M





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Re: trackable tracks / conversion

nathandunn

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  


Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: trackable tracks / conversion

Michael Paulini
Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  


Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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: trackable tracks / conversion

nathandunn

If type types mapped directly, it may not be too bad.  I added this issue here:


Nathan


On Feb 20, 2018, at 5:41 AM, Michael Paulini <[hidden email]> wrote:

Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  

<Screen Shot 2018-02-20 at 5.21.29 AM.png><Screen Shot 2018-02-20 at 5.22.37 AM.png>

Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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: trackable tracks / conversion

nathandunn

Michael,

To clarify, you’d want to be able to specify it in the track type, for instance, such that an entire track would automatically encode a particular biotype by default when dragging up.

e.g., 

{
    "key" : "Official Gene Set v3.2 Canvas",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Official Gene Set v3.2/{refseq}/trackData.json”,
      “biotype”:”ncRNA"
}

?
 

Nathan


On Feb 20, 2018, at 6:55 AM, Nathan Dunn <[hidden email]> wrote:


If type types mapped directly, it may not be too bad.  I added this issue here:


Nathan


On Feb 20, 2018, at 5:41 AM, Michael Paulini <[hidden email]> wrote:

Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  

<Screen Shot 2018-02-20 at 5.21.29 AM.png><Screen Shot 2018-02-20 at 5.22.37 AM.png>

Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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/
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Re: trackable tracks / conversion

Michael Paulini
Yes, that is what I am after.

M

On 20/02/18 22:30, Nathan Dunn wrote:

Michael,

To clarify, you’d want to be able to specify it in the track type, for instance, such that an entire track would automatically encode a particular biotype by default when dragging up.

e.g., 

{
    "key" : "Official Gene Set v3.2 Canvas",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Official Gene Set v3.2/{refseq}/trackData.json”,
      “biotype”:”ncRNA"
}

?
 

Nathan


On Feb 20, 2018, at 6:55 AM, Nathan Dunn <[hidden email]> wrote:


If type types mapped directly, it may not be too bad.  I added this issue here:


Nathan


On Feb 20, 2018, at 5:41 AM, Michael Paulini <[hidden email]> wrote:

Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  

<Screen Shot 2018-02-20 at 5.21.29 AM.png><Screen Shot 2018-02-20 at 5.22.37 AM.png>

Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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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Re: trackable tracks / conversion

nathandunn

This should be implemented here:


I also allowed for automatic inference, as well.  Still under review, so feel free to provide feedback.

Nathan

On Feb 21, 2018, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Yes, that is what I am after.

M

On 20/02/18 22:30, Nathan Dunn wrote:

Michael,

To clarify, you’d want to be able to specify it in the track type, for instance, such that an entire track would automatically encode a particular biotype by default when dragging up.

e.g., 

{
    "key" : "Official Gene Set v3.2 Canvas",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Official Gene Set v3.2/{refseq}/trackData.json”,
      “biotype”:”ncRNA"
}

?
 

Nathan


On Feb 20, 2018, at 6:55 AM, Nathan Dunn <[hidden email]> wrote:


If type types mapped directly, it may not be too bad.  I added this issue here:


Nathan


On Feb 20, 2018, at 5:41 AM, Michael Paulini <[hidden email]> wrote:

Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  

<Screen Shot 2018-02-20 at 5.21.29 AM.png><Screen Shot 2018-02-20 at 5.22.37 AM.png>

Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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.






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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.






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Re: trackable tracks / conversion

Michael Paulini
Will have to give it a spin. Especially the "auto" bit.

thanks,

M

On 22/02/18 16:28, Nathan Dunn wrote:

This should be implemented here:


I also allowed for automatic inference, as well.  Still under review, so feel free to provide feedback.

Nathan

On Feb 21, 2018, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Yes, that is what I am after.

M

On 20/02/18 22:30, Nathan Dunn wrote:

Michael,

To clarify, you’d want to be able to specify it in the track type, for instance, such that an entire track would automatically encode a particular biotype by default when dragging up.

e.g., 

{
    "key" : "Official Gene Set v3.2 Canvas",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Official Gene Set v3.2/{refseq}/trackData.json”,
      “biotype”:”ncRNA"
}

?
 

Nathan


On Feb 20, 2018, at 6:55 AM, Nathan Dunn <[hidden email]> wrote:


If type types mapped directly, it may not be too bad.  I added this issue here:


Nathan


On Feb 20, 2018, at 5:41 AM, Michael Paulini <[hidden email]> wrote:

Ideally, it would keep the annotation type, so it would be possible to drag a repeat feature into the track and it stays a repeat feature.
Maybe based on the biotype or some config variable in the tracklist. Because else it creates non-sensical CDSes, which as you said need right clicking and more manual intervention.

M


On 20/02/18 13:22, Nathan Dunn wrote:

Michael,

You should be able to right-click on them or explicitly change the annotation once you drag it to the top.  

<Screen Shot 2018-02-20 at 5.21.29 AM.png><Screen Shot 2018-02-20 at 5.22.37 AM.png>

Or do you mean “can you keep the default type” when you drag it up?

Nathan


On Feb 20, 2018, at 3:12 AM, Michael Paulini <[hidden email]> wrote:

Hia,

I was looking for a way to prevent webapollo from converting tracks that are dragged into the curation area to CDSes and rather specify a biotype for them, so ncRNA tracks or genome features stay the type they are.

M




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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