I made a short document to show how you can create a searchable gene track
on mm10, starting from a UCSC gtf file. I convert it to a GFF3Tabix file
and then go through the "Add track" widget in JBrowse Desktop making sure
to add the gene_name field for indexing (see screenshots)
https://gist.github.com/cmdcolin/30f3842c559c80253c3e7c250f94a7b5
-Colin
On Mon, May 23, 2022 at 1:21 PM Chang, Hsi <xz...@iu...> wrote:
> is there a way i can add a gene track? or on the webserver?
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Monday, May 23, 2022 3:15 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...
> >
> *Subject:* Re: [Gmod-ajax] [External] Re: Inquiry
>
> You don't often get email from col...@gm.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2
> desktop, but we have not fleshed it out as a resource and it does not yet
> have a gene track or gene names indexed
>
>
> We can definitely add this to our todo list!
>
>
>
> -Colin
>
> On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...> wrote:
>
> Please keep the JBrowse mailing list looped in, since more eyes==more
> chance of finding the problem!
>
> Is this in the desktop application or the webserved JBrowse? Can you send
> a jbrowse.conf file (which you would have if it's a web application)?
> Troubleshooting the desktop application might be a little harder, but I
> imagine there is a problem configuring the search index. If you're using
> the desktop version, can you send a screenshot of the configuration window
> around configuring search for the mouse genome?
>
> On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:
>
> I test on my laptop. Yes, i am not able to put a gene name into the box
> instead only coordinate.
> No problem when using the human genome.
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 1:36 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi,
>
> Can you give us a little more information? Is this in a publicly available
> JBrowse instance? Can you give us a URL? When you write "Select the
> region", are you searching for something and it isn't working?
>
> Thanks,
> Scott
>
>
> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>
> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
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