Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

[Nathan D. <nat...@lb...>]

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:

https://github.com/GMOD/Apollo/issues/2034 <https://github.com/GMOD/Apollo/issues/2034>

Nathan


> On Feb 7, 2019, at 9:52 AM, Rob Syme <rob...@gm...> 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 <nat...@lb... <mailto:nat...@lb...>> 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 <rob...@gm... <mailto:rob...@gm...>> 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 <http://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 <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/ <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 sy...@li... <mailto:sy...@li...> | 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/ <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 sy...@li... <mailto:sy...@li...> | 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 sy...@li... | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
>