Re: [Gmod-ajax] VL: JBowse

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

If you need the whole genome, it may be advisable to ask the creator of the
instance to provide you the  BED file they used to load it originally


-Colin



On Fri, May 21, 2021 at 7:46 AM Jenni Tolppanen (TAU) <
jen...@tu...> wrote:

>
>
> ------------------------------
> *Lähettäjä:* Jenni Tolppanen (TAU) <jen...@tu...>
> *Lähetetty:* torstai 6. toukokuuta 2021 9.31
> *Vastaanottaja:* Scott Cain <sc...@sc...>
> *Aihe:* VS: [Gmod-ajax] JBowse
>
> Hi,
>
> Thank you for the quick response!
>
> What should I do if I want BED files? And is it possible to obtain BED
> file from all the genome at once?
>
> -Jenni
> ------------------------------
> *Lähettäjä:* Scott Cain <sc...@sc...>
> *Lähetetty:* torstai 22. huhtikuuta 2021 23.09
> *Vastaanottaja:* Jenni Tolppanen (TAU) <jen...@tu...>
> *Kopio:* gmo...@li... <gmo...@li...>
> *Aihe:* Re: [Gmod-ajax] JBowse
>
> Hi Jenni,
>
> That is very strange--I've never seen that dialog box look like that.
> There are two options in that box: Visible region or whole reference
> sequence which correspond to the two circles you can check off (with
> visible region selected by default and selected in the picture you sent).
> Even though the text is very "smooshed" the dialog box should still work,
> so you can select either of the circles and click "Save" and it will save a
> GFF3 file with the data to your computer.
>
> Please let us know if you have any problems with this,
> Scott
>
>
> On Thu, Apr 22, 2021 at 12:42 PM Jenni Tolppanen (TAU) <
> jen...@tu...> wrote:
>
> Hi,
>
> I have a problem when I try to download data from the browser. For example
> I would like to get all common putative enhancers. Attached picture shows
> the problem. What should I do?
>
> Yours faithfully,
>
> Jenni Tolppanen
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>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
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