https://github.com/cmdcolin/colorbycds

A JBrowse plugin to color the features and DNA track according the coding frame
https://github.com/cmdcolin/colorbycds

Last synced: 10 months ago
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A JBrowse plugin to color the features and DNA track according the coding frame

• Host: GitHub
• URL: https://github.com/cmdcolin/colorbycds
• Owner: cmdcolin
• Created: 2017-08-02T15:29:12.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2018-10-11T15:48:44.000Z (over 7 years ago)
• Last Synced: 2025-03-04T23:31:42.978Z (over 1 year ago)
• Language: JavaScript
• Homepage:
• Size: 5.16 MB
• Stars: 2
• Watchers: 3
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog.md

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README

          
# colorbycds

A JBrowse plugin for viewing the frame that a coding sequences of a gene is in and coloring the DNA track and gene appropriately

## Screenshot

![](img/1.png)

Figure: Picture of genes and the DNA track with the plugin enabled. The coloring of the CDS boxes corresponds to the colored rows of the DNA track

## Example

    {

     "label" : "genes",

     "urlTemplate" : "tracks/genes/{refseq}/trackData.json",

     "storeClass" : "JBrowse/Store/SeqFeature/NCList",

     "type" : "CanvasFeatures",

     "glyph" : "ColorByCDS/View/FeatureGlyph/Gene"

    }

Note that if you loaded your data with two levels e.g. mRNA->exon/cds instead of three levels e.g. gene->mRNA->exon/cds then use "ColorByCDS/View/FeatureGlyph/ProcessedTranscript" as the glyph, otherwise you will see your feature is exploded into tiny pieces and not connected by introns.

## Installation

Download to plugins/ColorByCDS and add

    "plugins": ["ColorByCDS"]

to jbrowse_conf.json or trackList.json. See JBrowse FAQ on installing plugins for more details

## Notes

Relies on the phase field (column 8) of your GFF to be calculated correctly. Use genometools `gt gff3 -tidy yourfile.gff > yourfile_fixed.gff` to recalculate phase properly