README.md

SeqLighter v1.0

How to Cite

Description

SeqLighter is a dynamic sequence viewer plugin implemented using the BioJS framework.

The plugin is currently set up to work with feature tracks that use the trackType HTMLFeatures, and represent the featureType mRNA and their subfeatures (five_prime_UTR, three_prime_UTR, exon, CDS).

First, the input GFF3 file would need to be processed like so:

$ bin/flatfile-to-json.pl --gff data/raw/genes.gff3 --out data/json/arabidopsis \
  --trackLabel athaliana_genes --key 'A. thaliana Gene Models' \
  --nameAttributes "name,alias,id" --trackType "JBrowse/View/Track/HTMLFeatures" \
  --type "mRNA" --subfeatureClasses '{ "exon": "transcript-exon", "CDS": "transcript-CDS", 
  "five_prime_UTR" : 	"transcript-UTR", "three_prime_UTR" : "transcript-UTR" }'

Second, the plugin can be enabled using either of the following methods (see official JBrowse documentation on using plugins):

tracks.conf

	[plugins]
	SeqLighter.location += ./plugins/SeqLighter

trackList.json

	"plugins": {
		"SeqLighter" : { "location" : "./plugins/SeqLighter" }
	}

Third, the plugin can be associated with a gene model track by adding a right click menu option (by updating the track configuration stanza) to trigger the sequence displayer in a popup contentDialog:

trackList.json

{
	"label" : "athaliana_genes",
    "key" : "A. thaliana Gene Models",
    "storeClass" : "JBrowse/Store/SeqFeature/NCList",
    "trackType" : null,
    "type" : "FeatureTrack",
    "urlTemplate" : "tracks/athaliana_genes/{refseq}/trackData.json",
    "style" : {
    	"className" : "feature"
    	"subfeatureClasses": {
       		"exon": "transcript-exon",
     		"CDS": "transcript-CDS",
     		"five_prime_UTR" : "transcript-UTR",
     		"three_prime_UTR" : "transcript-UTR"
     	}
    }
	"menuTemplate" : [
    	{
           "content" : "function(track,feature,div ){ return SequenceViewer(track, feature, div); }",
           "iconClass" : "dijitIconDatabase",
           "action" : "contentDialog",
           "label" : "View Sequence"
        }  
    	],
    	"compress" : 0
    },
}

Finally, on successful configuration, the sequence viewer can be launched via a Right-Click (or Ctrl + Left-Click on a Mac) the gene model track. Then, select View Sequence in the drop down menu.

Contributors

• Maria Kim - JCVI
• Vivek Krishnakumar - JCVI

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If you have any questions regarding the usage of this plugin, please write to mailto:araport@jcvi.org