should provide neat html features and/or paired end reads for BAM tracks

[nathandunn]

Related to this conversations: http://gmod.827538.n3.nabble.com/Request-for-clarification-on-draggable-BAM-tracks-td4060195.html

Neat Features used to properly draw the introns. If I create NeatAlignments, however, there are some class problems that need to be solved with the new track types.

[nathandunn]

There are two options for this:

1 - enable neat features for BAMS. We did this neat features this way:

https://github.com/GMOD/Apollo/blob/master/client/apollo/js/View/Track/DraggableNeatHTMLFeatures.js

We would extend this instead:

https://github.com/GMOD/Apollo/blob/master/client/apollo/js/View/Track/DraggableAlignments.js

That being said, there were some ClassNotFound errors in the original NeatFeatures code (not in the original code), so either need to fix it there, or over-ride it in the new DraggableNeatAlignments class.

2 - employ paired end reads in the HTML alignment tracks, by either fixing the JBrowse Alignments in JBrowse, fixing it in the apollo draggable track. @cmdcolin did this for Canvas, though its probably more than we need:

https://github.com/GMOD/jbrowse/pull/1235/files#diff-4e9bd0916dfb5f75b9a47bc463e870a5

===

I'll probably attempt version 1 again later this week.

[cmdcolin]

paired read isn't necessary to display splicing. I think that, if you just apply the "track transformer" code in main.js to change Alignments2 to DraggableAlignments it should work. I would also probably not use neatfeatures on the alignments but that is preference I suppose

[nathandunn]

@cmdcolin I think the goal was to show to display the splicing, but still have the track draggable, but as DraggableAlignments inherits from Alignments (both HTMLFeatures), it doesn't display the splicing (but is draggable).

That being said, while I like Neat Features for displaying predictions, I agree that they are a bit noisy for displaying read data, but any display is better than none.

[robsyme]

@cmdcolin - I think that the difficulty is that tracks converted into WebApollo/View/Track/DraggableAlignments don't display gapped reads correctly. For example, RNAseq reads spanning an intron are rendered as a single block spanning the intron:

{
   "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}-"
      },
      {
         "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"
      }
    ]
}

In this case, the reads in Track/Alignments are converted into DraggableAlignments.

[cmdcolin]

Interesting thanks for testing that @robsyme

I checked in JBrowse 1 and it does still display spliced RNA-seq alignments with the HTML version JBrowse/View/Track/Alignments class

[nathandunn]

@cmdcolin This might be easy to fix then if its just a bug in the Apollo DraggableAlignments code. Is this data part of the volvox sample data?

[nathandunn]

Running this data: https://github.com/elsiklab/sashimiplot/tree/master/test/data

[robsyme]

FYI, The image above was using:

• JBrowse 1.16.2-release
• Webapollo 2.3.0 (e7adf93)

[nathandunn]

Canvas on the top (translate to the WebApolloAlignments2) versus the HTML on the bottom translated to DraggableAlignment.

[nathandunn]

duped @cmdcolin results in JBrowse:

[nathandunn]

Looks like a lot of the problems are CSS related from very very old code. This is a first-pass based on #2035 :

[robsyme]

That was quick! I've checked this on my instance and it does make split reads clear.

The complication is that annotations created from these reads do not retain the (implied) intron when dragged to the User-created annotations track:

I hate to add things to your list, but is it possible (at whatever time) for split reads to create two or more CDS features?

[nathandunn]

I think this was broken before (you’re right, I did not fix that part) in both Canvas and HTML versions. Would you mind opening a separate bug for this? Nathan

…

On Feb 7, 2019, at 1:55 PM, Robert Syme ***@***.***> wrote: That was quick! I've checked this on my instance and it does make split reads clear. The complication is that annotations created from these reads do not retain the (implied) intron when dragged to the User-created annotations track: <https://user-images.githubusercontent.com/31576/52444649-fa3af500-2af6-11e9-80d6-ddaac34eef02.gif> I hate to add things to your list, but is it possible (at whatever time) for split reads to create two or more CDS features? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#2034 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qrcX-yYyVYMGy_bLWN5Ov1ckMMEQks5vLKDngaJpZM4an1WH>.

[robsyme]

Done (#2036). Thanks Nathan!

[nathandunn]

@robsyme This should now be fixed. I only fixed this for mRNA, but you can change the annotation type if you need to.

If doing this for non-coding RNA's is something that is fairly common you do (thus changing the annotation type constantly becomes a pain), let me know and I can fix that as well.

[robsyme]

Perfect. I've just updated our instance and dragging reads to create new annotations works as expected. Thanks Nathan!
Congratulations on the new manuscript, btw. Great work.