Re: [Gmod-ajax] Installing SashimiPlot for JBrowse1

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

The blue corresponds to negative strand and brown to positive strand, which
matches up with in the screenshot that it is brown matching the positive
strand gene, blue with negativetsas

I updated the README of the plugin to try to help clarify that

-Colin

On Fri, Apr 30, 2021 at 12:03 PM Hans Vasquez-Gross <
hav...@uc...> wrote:

> Hi Colin,
>
> Thank you, re-running setup.sh did the trick.
>
> I got a question regarding SashimiPlot.  I know the opacity of the line is
> a measurement of number of reads that support the junction point. However,
> do the different colors signify anything? I'm guessing it just switches
> between blue/brown to easily distinguish between different genes?
>
> [image: Screenshot from 2021-04-30 08-58-04.png]
>
>
> Thank you,
> -Hans
>
> On Thu, Apr 29, 2021 at 6:07 PM Colin <col...@gm...> wrote:
>
>> You may need to re-run setup.sh after downloading SashimiPlot to the
>> plugins/SashimiPlot folder
>>
>> Another faq entry to help explain...
>> https://jbrowse.org/docs/faq.html#how-do-i-use-plugins-with-jbrowse
>>
>> Hope that helps :)
>> -Colin
>>
>> On Thu, Apr 29, 2021 at 8:48 PM Hans Vasquez-Gross via Gmod-ajax <
>> gmo...@li...> wrote:
>>
>>> Hi JBrowse team,
>>>
>>> I am trying to install SashimiPlot plugin in JBrowse. I already have
>>> another plugin enabled on JBrowse (VariantEffectPlugin), so plugins are
>>> generally working. I performed the same steps to enable it.
>>>
>>> 1) In the plugins folder, cloned the git repo
>>> 2) Renamed git folder from sashimiplot to SashimiPlot
>>> 3) Added configuration to jbrowse.conf
>>>
>>> [ plugins.SashimiPlot ]
>>> location = plugins/SashimiPlot
>>> [ plugins.VariantEffectPlugin ]
>>> location = plugins/VariantEffectPlugin
>>>
>>> 4) Added track configuration to tracks.conf
>>>
>>> [tracks.pachon_adult_ovary_rep2_bam]
>>> urlTemplate=pachon_adult_ovary_n7.rep2.sorted.bam
>>> storeClass=JBrowse/Store/SeqFeature/BAM
>>> type=SashimiPlot/View/Track/Sashimi
>>> chunkSizeLimit = 50000000
>>> useXS = true
>>> category = Sashimi
>>> label = Pachon Adult Ovary rep2 sashimi
>>>
>>>
>>> The result is the following screenshot.
>>> [image: Screenshot from 2021-04-29 17-40-44.png]
>>>
>>>
>>> Did I do something wrong during the installation?
>>>
>>> Thank you,
>>> -Hans
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
> --
> Hans Vasquez-Gross
> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
> PhD Candidate
> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
> Department of Plant Science
> University of California at Davis
> Email: hav...@uc...
> Skype: hansvg.ucd
>