Re: [Gmod-ajax] visualization of split alignments

[Colin <col...@gm...>]

Hi there,
I think this question came through our gitter chat earlier but I'll repeat
what we said there

The screenshot showing that "Link supplementary reads" functionality was an
older demo for a poster, but it was a bit hacky so it didn't end up getting
merged unfortunately!

I put in a new feature request for this though as it would be a very useful
feature https://github.com/GMOD/jbrowse-components/issues/4659

Some alternatives to get this functionality "today" using jbrowse would be
to use the "breakpoint split view"

It can draw connections between reads in the "single row" mode. The
screenshot below shows this
[image: image.png]


[image: image.png]

There are also the "read cloud" and "read arcs" modes but these are a bit
weirder for long reads. Hope that helps, I can update this thread if we add
the "Link supplementary reads" functionality

-Colin

On Fri, Nov 15, 2024 at 11:18 AM Robert Månsson Welinder <
rob...@sc...> wrote:

> Hi,
>
> Started playing around with looking at PacBio long-read data in JBrowse 2
> (2.16.1).
>
> How do I find the option that is called "link samplementary reads" in the
> JBrowse 2 demo?
> [image: Screenshot 2024-11-15 at 13.10.28.png]
>
> [Link to demo:
> https://s3.amazonaws.com/jbrowse.org/code/jb2/beta/skbr3_demo/index.html?config=test_data%2Fconfig_demo.json&session=share-4e68d7667f204ee4dfaf01279ee488275686147d4c93c86a80fb2994ad6c43c6&password=c17703b]c1fc0d1c7508bc1af8cf42892)
>
>
> Basically looking at translocations affecting the Immunoglobulin heavy
> chain locus and then one would like the VDJ recombination events to be
> linked via "lines" as shown above for "Link supplementary reads" while the
> actual translocations are shows using the "top/bottom split-view".
>
> Thanks in advance / Robert
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