Command to display marker track in Apollo

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Command to display marker track in Apollo

abhijit.synl@gmail.com
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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Re: Command to display marker track in Apollo

nathandunn

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 <[hidden email]> 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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Re: Command to display marker track in Apollo

Colin
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}' 


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

Screenshot from 2020-06-03 13-02-35.png


-Colin


On Tue, Jun 2, 2020 at 10:36 AM Nathan Dunn <[hidden email]> 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 <[hidden email]> 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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Re: Command to display marker track in Apollo

Colin
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 <[hidden email]> 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}' 


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

Screenshot from 2020-06-03 13-02-35.png


-Colin


On Tue, Jun 2, 2020 at 10:36 AM Nathan Dunn <[hidden email]> 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 <[hidden email]> 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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