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

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

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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