Re: [Gmod-ajax] Paired read and split read arc view

[Ke J. <bio...@gm...>]

Hi, Colin,

Great docs and function! They’re very helpful! Thanks for the update!

Thanks!

Ke

On Fri, Jan 3, 2025 at 11:39 AM Colin <col...@gm...> wrote:

> Hi Ke,
> Thanks for asking...I have been meaning to make a detailed documentation
> guide for these features.
>
> Here is a short writeup explaining the different ways to launch the
> breakpoint split view a gist form
> https://gist.github.com/cmdcolin/274040cff8a49c9e5265c4fa64265748
>
> The TLDR is that you can either launch the "breakpoint split view" from
>
> 1) the "SV inspector"
> 2) the feature details panels from clicking on reads or variant calls from
> a normal "linear genome view"
>
>
> I am going to try to polish this up and add this to our jbrowse.org docs
>
>
> -Colin
>
> On Thu, Jan 2, 2025 at 7:52 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I noticed that there is a new visualization mode for breakpoint split
>> view to show paired read and split read orientations added in the update
>> from Sep. 2024. This could be a very useful tool for us to explore
>> potential larger scale SVs. There is not much information/docs about how
>> this feature is turned on, and what kind of data is needed for this
>> feature. From the Blog post, it seems we need both SV calls (VCFs?) and
>> alignment tracks for this? How do we turn this view on with these tracks?
>>
>> Thanks!
>>
>> Ke
>>
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