Re: [Gmod-ajax] [apollo] Command to display marker track in Apollo

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

Meant to link to this documentation page not localhost
https://jbrowse.org/docs/html_features.html  :)

-Colin

On Wed, Jun 3, 2020 at 1:02 PM Colin <col...@gm...> wrote:

> Here is a command I used to load triangle shaped markers with HTMLFeatures
> on JBrowse
>
>
> bin/flatfile-to-json.pl --bed here.bed --bed here.bed --out
> sample_data/json/volvox --trackLabel MyTrack --className "triangle hgred"
> --clientConfig '{"arrowheadClass":null}'
>
> http://localhost:3000/docs/html_features.html
>
> I had to manually pass clientConfig for arrowheadClass instead of
> --arrowheadClass because of setting null properly on it to disable the
> strand arrows
>
> Screenshot here
>
> [image: Screenshot from 2020-06-03 13-02-35.png]
>
>
> -Colin
>
>
> On Tue, Jun 2, 2020 at 10:36 AM Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Abhjit,
>>
>> I am going to expand this to the JBrowse general mailing list as this is
>> more of a JBrowse question.
>>
>> I’ve never actually tried to do this specifically.
>>
>> If for some reason you get this to work in JBrowse, but not Apollo,
>> please let me know.
>>
>> Nathan
>>
>>
>>
>> On Jun 2, 2020, at 6:59 AM, Abhijit Sanyal <abh...@gm...>
>> wrote:
>>
>> Hello All,
>>
>> I would like to display markers on Apollo as tracks. I am still a novice
>> in using Apollo, so still learning the basics. I have the following command
>> for displaying gene tracks
>>
>> /app/Apollo/bin/flatfile-to-json.pl --gff /Apollo-TEMP/displayname.gff3
>> --arrowheadClass trellis-arrowhead --subfeatureClasses
>> '{"CDS":"pink-90pct", "five_prime_UTR":"purple-60pct",
>> "three_prime_UTR":"purple-60pct", "exon":"container-100pct"}' --className
>> container-16px --type mRNA --trackLabel Gene-Models --out
>> /apollo-annotation/genome/maize/Annot1/data/
>>
>> I would like to modify that to display SNP markers as arrowheads or
>> little triangles, and other genetic markers as rectangles, both magenta in
>> colour. I have gotten as far as below. Need a little help modifying the
>> rest of the code.
>>
>> /app/Apollo/bin/flatfile-to-json.pl --gff
>> /Apollo-TEMP/gsap645_markers.gff3 --arrowheadClass trellis-arrowhead
>> --className ?? --type genetic_marker --key blast --subfeatureClasses
>> '{"??"}' --trackLabel GENETIC-MARKER --out
>> /apollo-annotation/genome/maize/Annot1/data/
>>
>> The "??" are the places where I do not know what value to put, in order
>> to get the desired effect of triangle or a rectangle. Also I do not know
>> where to specify the color. Thank you for your help
>>
>> -Abhijit
>>
>>
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>