Request for clarification on draggable BAM tracks

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Request for clarification on draggable BAM tracks

Rob Syme
Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme




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: Request for clarification on draggable BAM tracks

nathandunn

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan







On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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: Request for clarification on draggable BAM tracks

Rob Syme
Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:

Screenshot from 2019-02-07 12-42-28.png


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}


Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <[hidden email]> wrote:

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan







On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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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Re: Request for clarification on draggable BAM tracks

nathandunn

Rob,

I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 

I’ll take a look at getting one, if not both working:


Nathan


On Feb 7, 2019, at 9:52 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:

<Screenshot from 2019-02-07 12-42-28.png>


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}


Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <[hidden email]> wrote:

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan



<PastedGraphic-1.png>



On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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.






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: Request for clarification on draggable BAM tracks

Rob Syme
Hi Nathan.

If you point in me (vaguely) the right direction, I might be able to have a look myself (if that would be helpful). Will certainly send a PR if I make any progress.

-rob

On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <[hidden email]> wrote:

Rob,

I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 

I’ll take a look at getting one, if not both working:


Nathan


On Feb 7, 2019, at 9:52 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:

<Screenshot from 2019-02-07 12-42-28.png>


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}


Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <[hidden email]> wrote:

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan



<PastedGraphic-1.png>



On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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.





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: Request for clarification on draggable BAM tracks

nathandunn



Please let me know if you need more help either there or. in the GH issue directly. 

Cheers,

Nathan



On Feb 7, 2019, at 10:03 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan.

If you point in me (vaguely) the right direction, I might be able to have a look myself (if that would be helpful). Will certainly send a PR if I make any progress.

-rob

On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <[hidden email]> wrote:

Rob,

I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 

I’ll take a look at getting one, if not both working:


Nathan


On Feb 7, 2019, at 9:52 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:

<Screenshot from 2019-02-07 12-42-28.png>


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}


Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <[hidden email]> wrote:

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan



<PastedGraphic-1.png>



On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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.





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.






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: Request for clarification on draggable BAM tracks

nathandunn

This is fixed on on Apollo’s master branch per this PR:


Let me know if there are any problems with it. 

Cheers,

Nathan


On Feb 7, 2019, at 11:55 AM, Nathan Dunn <[hidden email]> wrote:




Please let me know if you need more help either there or. in the GH issue directly. 

Cheers,

Nathan



On Feb 7, 2019, at 10:03 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan.

If you point in me (vaguely) the right direction, I might be able to have a look myself (if that would be helpful). Will certainly send a PR if I make any progress.

-rob

On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <[hidden email]> wrote:

Rob,

I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 

I’ll take a look at getting one, if not both working:


Nathan


On Feb 7, 2019, at 9:52 AM, Rob Syme <[hidden email]> wrote:

Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:

<Screenshot from 2019-02-07 12-42-28.png>


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}


Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <[hidden email]> wrote:

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan



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On Feb 6, 2019, at 8:25 AM, Rob Syme <[hidden email]> wrote:

Hi all

I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.

I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA

Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.

Rob Syme



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