highlighting of matching intron/exon boundaries between reads and genes in user created content track

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highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;">highlight_matching_boundaries.jpg




Hi,

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks.
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting.

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you.

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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json


Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <[hidden email]> wrote:

<a imageanchor="1" href="about:invalid#zClosurez" style="margin: 0px 1em 1em 0px; padding: 0px; border: 0px none; text-decoration: none; color: rgb(102, 17, 204); cursor: text; clear: left; float: left;" class=""><highlight_matching_boundaries.jpg>
<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>

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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S
Hi Nathan,

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types?


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="jMeq6m9bAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>


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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  http://demo.genomearchitect.org/Apollo2/annotator/index ([hidden email] / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager RNA-Seq reads" class="">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <[hidden email]> wrote:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json


Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@gmail.com> wrote:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>




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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S

no_plugins.PNG


Hi Nathan,

We did not have the WebApollo plugin that is mentioned in the linked issue.

We did have the following plugins defined:

"plugins": [
       
"NeatHTMLFeatures",
       
"NeatCanvasFeatures",
       
"HideTrackLabels"
   
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  Are these plugins not needed anymore in Apollo 2.5.0?
Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  <a href="http://demo.genomearchitect.org/Apollo2/annotator/index" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/index (<a href="javascript:" target="_blank" gdf-obfuscated-mailto="9XfxUyySAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">demo@... / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager+RNA-Seq+reads" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="9XfxUyySAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn




On Mar 31, 2020, at 9:44 AM, Wim S <[hidden email]> wrote:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons. 

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:


Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).


My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@gmail.com> wrote:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json


Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@gmail.com> wrote:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>

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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S
According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6.
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation.


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="3odyS_WhAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons. 

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:

<a href="https://github.com/GMOD/Apollo/issues/2416" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  <a href="http://demo.genomearchitect.org/Apollo2/annotator/index" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/index (<a href="javascript:" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" gdf-obfuscated-mailto="3odyS_WhAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">d<a href="javascript:" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" gdf-obfuscated-mailto="3odyS_WhAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">emo@... / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager+RNA-Seq+reads" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>


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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn

Thanks.   I have some older instances up via AWS. 


My plan is to take a look at it later this week or next week.

Nathan


On Apr 1, 2020, at 5:36 AM, Wim S <[hidden email]> wrote:

According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6. 
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation. 


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <wim...@gmail.com> wrote:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:


Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).


My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@gmail.com> wrote:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json


Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@gmail.com> wrote:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>




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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn
After poking around some more, we couldn't find a great solution.

I could get it working, but I had to:

(a) configure loading JBrowse 1.15.4 (I didn't do extensive testing though)

and 


If we get more time there might be a way to add it back, but most likely it won't get fixed in the immediate future, unfortunately. 


On Wednesday, April 1, 2020 at 8:41:08 AM UTC-7, Nathan Dunn wrote:

Thanks.   I have some older instances up via AWS. 

I added a note here: <a href="https://github.com/GMOD/Apollo/issues/2416" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

My plan is to take a look at it later this week or next week.

Nathan


On Apr 1, 2020, at 5:36 AM, Wim S <[hidden email]> wrote:

According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6. 
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation. 


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:

<a href="https://github.com/GMOD/Apollo/issues/2416" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  <a href="http://demo.genomearchitect.org/Apollo2/annotator/index" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/index ([hidden email][hidden email] / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager+RNA-Seq+reads" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>




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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S
Thank you having a look and the information.

Op vrijdag 10 april 2020 01:59:53 UTC+2 schreef Nathan Dunn:
After poking around some more, we couldn't find a great solution.

I could get it working, but I had to:

(a) configure loading JBrowse 1.15.4 (I didn't do extensive testing though)

and 

(b) add code removed here: <a href="https://github.com/GMOD/Apollo/commit/5a3cde3ee1" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fcommit%2F5a3cde3ee1\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGcbSaA1-QPm4jDRXAoEtl3yEzAzw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fcommit%2F5a3cde3ee1\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGcbSaA1-QPm4jDRXAoEtl3yEzAzw&#39;;return true;">https://github.com/GMOD/Apollo/commit/5a3cde3ee1 

If we get more time there might be a way to add it back, but most likely it won't get fixed in the immediate future, unfortunately. 


On Wednesday, April 1, 2020 at 8:41:08 AM UTC-7, Nathan Dunn wrote:

Thanks.   I have some older instances up via AWS. 

I added a note here: <a href="https://github.com/GMOD/Apollo/issues/2416" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

My plan is to take a look at it later this week or next week.

Nathan


On Apr 1, 2020, at 5:36 AM, Wim S <<a href="javascript:" rel="nofollow" target="_blank" gdf-obfuscated-mailto="sgtl6EV1AAAJ" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6. 
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation. 


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:

<a href="https://github.com/GMOD/Apollo/issues/2416" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  <a href="http://demo.genomearchitect.org/Apollo2/annotator/index" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/index (<a href="javascript:" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" rel="nofollow" target="_blank" gdf-obfuscated-mailto="sgtl6EV1AAAJ" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">d<a href="javascript:" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" rel="nofollow" target="_blank" gdf-obfuscated-mailto="sgtl6EV1AAAJ" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">emo@... / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager+RNA-Seq+reads" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>





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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

Wim S
Hi Nathan

It turns out that this feature is quite essential to our users. I do also find it a bit strange that other users don't miss this feature.

A work around currently adopted by some of our users is using a physical geometry ruler against the monitor to see which reads/features share the same exon boundaries.
This can't be the intention of the software.

Is there a way to increase the priority of this feature?

Thank you.

Wim



Op woensdag 15 april 2020 20:11:08 UTC+2 schreef Wim S:
Thank you having a look and the information.

Op vrijdag 10 april 2020 01:59:53 UTC+2 schreef Nathan Dunn:
After poking around some more, we couldn't find a great solution.

I could get it working, but I had to:

(a) configure loading JBrowse 1.15.4 (I didn't do extensive testing though)

and 

(b) add code removed here: <a href="https://github.com/GMOD/Apollo/commit/5a3cde3ee1" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fcommit%2F5a3cde3ee1\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGcbSaA1-QPm4jDRXAoEtl3yEzAzw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fcommit%2F5a3cde3ee1\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGcbSaA1-QPm4jDRXAoEtl3yEzAzw&#39;;return true;">https://github.com/GMOD/Apollo/commit/5a3cde3ee1 

If we get more time there might be a way to add it back, but most likely it won't get fixed in the immediate future, unfortunately. 


On Wednesday, April 1, 2020 at 8:41:08 AM UTC-7, Nathan Dunn wrote:

Thanks.   I have some older instances up via AWS. 

I added a note here: <a href="https://github.com/GMOD/Apollo/issues/2416" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

My plan is to take a look at it later this week or next week.

Nathan


On Apr 1, 2020, at 5:36 AM, Wim S <[hidden email]> wrote:

According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6. 
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation. 


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:

<a href="https://github.com/GMOD/Apollo/issues/2416" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2416\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF826X1XcQEdnWFoQkI7gojhMQgBA&#39;;return true;">https://github.com/GMOD/Apollo/issues/2416

Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

I tested this affect in 2.5.0 on our honeybee demo and it works:  <a href="http://demo.genomearchitect.org/Apollo2/annotator/index" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2Findex\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFtTzfJMzHLi9JU9pBse302N1HDkQ&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/index (d[hidden email] / demo ) <a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&amp;organism=3836&amp;tracks=Forager+RNA-Seq+reads" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup2.19%3A2418548..2419313%26organism%3D3836%26tracks%3DForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw6iOpuURYridy3KP5JHh93P22Qw&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group2.19:2418548..2419313&organism=3836&tracks=Forager%20RNA-Seq%20reads

My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json

<a href="https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY&#39;;return true;">https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/Y6maCsbCnDY

Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@<a href="http://gmail.com/" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" 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:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>





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Re: highlighting of matching intron/exon boundaries between reads and genes in user created content track

nathandunn

It is on the list, and I’m happy to take another look at it prior to releasing any maintenance fixes. 

However, you should be able to get the same affect by:

- using the 2.6.0 version of Apollo
- set JBrowse release version to 1.15.4 (current version is 1.16.9)
- applying this patch to Apollo: https://github.com/GMOD/Apollo/commit/5a3cde3ee1

I’m happy to retest this for you if this is something you would be interested in doing. 

Nathan


On May 26, 2020, at 7:23 AM, Wim S <[hidden email]> wrote:

Hi Nathan

It turns out that this feature is quite essential to our users. I do also find it a bit strange that other users don't miss this feature.

A work around currently adopted by some of our users is using a physical geometry ruler against the monitor to see which reads/features share the same exon boundaries.
This can't be the intention of the software.

Is there a way to increase the priority of this feature?

Thank you.

Wim



Op woensdag 15 april 2020 20:11:08 UTC+2 schreef Wim S:
Thank you having a look and the information.

Op vrijdag 10 april 2020 01:59:53 UTC+2 schreef Nathan Dunn:
After poking around some more, we couldn't find a great solution.

I could get it working, but I had to:

(a) configure loading JBrowse 1.15.4 (I didn't do extensive testing though)

and 


If we get more time there might be a way to add it back, but most likely it won't get fixed in the immediate future, unfortunately. 


On Wednesday, April 1, 2020 at 8:41:08 AM UTC-7, Nathan Dunn wrote:

Thanks.   I have some older instances up via AWS. 


My plan is to take a look at it later this week or next week.

Nathan


On Apr 1, 2020, at 5:36 AM, Wim S <[hidden email]> wrote:

According to one of our main users of the Apollo system, the exon boundaries where also highlighted within RNAseq reads in Apollo 2.0.6. 
I can't (easily) double check this because already decommissioned our Apollo 2.06 installation. 


Op dinsdag 31 maart 2020 19:42:33 UTC+2 schreef Nathan Dunn:




On Mar 31, 2020, at 9:44 AM, Wim S <wim...@gmail.com> wrote:

<no_plugins.PNG>

Hi Nathan, 

We did not have the WebApollo plugin that is mentioned in the linked issue. 

We did have the following plugins defined:

"plugins": [
        
"NeatHTMLFeatures",
        
"NeatCanvasFeatures",
        
"HideTrackLabels"
    
],

Removing all these plugins did remove the black triangles, now a line is shown between the exons.  

Excellent! 

Are these plugins not needed anymore in Apollo 2.5.0?

They are now built in.  

There are some issues with duplicating these that we weren’t able to get around. 

Also highlighting of matching exon boundaries is back, at least between the gene model and genes predicted via stringtie based on just RNAseq.

In the reads though the matching exon boundaries are only shown if the read terminates at the exon boundary, not if the aligned read spans an intron.
Is that intended?

Yes, that was the original implementation (or that is my guess), which I’m going to guess hasn’t changed. 

However, I agree that it would be great if it highlighted the other parts of the read if possible.  I’m not sure if its possible, but I’ve added this just to take a look when someone has time:


Nathan



See also the screenshot.

Wim



Op dinsdag 31 maart 2020 14:53:17 UTC+2 schreef Nathan Dunn:

I apologize, it was a long day yesterday. For some reason I ignored the fact they were reads. 

Your initial track type was correct.  

Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).


My guess is that the misconfigured plugin (the extra blackness) is also breaking the highlights. 

Try removing that from the trackList.json (if its there) and let me know what you see. 

If it isn’t there, please send the trackList.json with a javascript console.log and I can see if there is another possible problem. 

Cheers,

Nathan


On Mar 31, 2020, at 5:33 AM, Wim S <wim...@gmail.com> wrote:

Hi Nathan, 

We currently have defined as tracktype:

"type": "WebApollo/View/Track/DraggableAlignments",

Switching type to one of the types below causes an error:
"type": "FeatureTrack",
"type": "HTMLFeature",

Do I need to prefix these track types with something (as is also the case for DraggableAlignments).

Do FeatureTrack and HTMLFeature have the same or similar functionality as DraggableAlignments?
And are the  implied introns and exons still shown? Can the reads still be dragged to the user created annotations track?

I am still a bit lost on which is now the recommended track type for visualising RNA-seq reads and using them to update a gene model in the user created annotations track. The functionality from the old Apollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", now seems to be spit over multiple different track types? 


Thank you also for the information about the "weird black lines". I'll try to remove the plugin from the trackList.json  (if present, we try to run as much with the defaults).

Op maandag 30 maart 2020 22:10:14 UTC+2 schreef Nathan Dunn:

Your track `type` should be `FeatureTrack` or `HTMLFeature` for the highlighting to work.


Also, please read this notice (it will fix your weird black lines) and remove the extra plugin entry from your trackList.json


Nathan


On Mar 30, 2020, at 5:24 AM, Wim S <wim...@gmail.com> wrote:

<Auto Generated Inline Image 2.jpeg>


Hi, 

In our Apollo 2.5.0 installation the matching intron/exon boundaries are not highlighted anymore between the reads and the genes in the user created content tracks. 
In our previous version of Apollo (2.0.6), upon selecting a read or a gene, the matching intron/exon boundaries were highlighted.

See the top left image for the expected behavior, and right for the situation without highlighting. 

Is there a way to re-enable the highlighting of matching intron/exon boundaries in Apollo 2.5.0?

Thank you. 
<highlight_matching_boundaries.jpg><Auto Generated Inline Image 2.jpeg>





<no_plugins.PNG>






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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].