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

[Nathan D. <nat...@lb...>]

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
>