JBrowseDev/The SubfeatureClasses Option

In order to make subfeatures appear in JBrowse, it is necessary to assign a genome.css class to them. This is done in with an association list in JSON syntax, where the key is the type of subfeature (e.g. CDS, UTR, match_part, mRNA), and the value is the genome.css class that will be used as the appearance of that subfeature.

As an example, the '--subfeatureClasses' argument to flatfile-to-json might look something like '{ "CDS" : "transcript-CDS", "UTR" : "transcript-UTR" }'. This could be rewritten as:

'{
   "CDS" : "transcript-CDS",
   "UTR" : "transcript-UTR"  
 }'

This second format makes the JSON structure more obvious, but the first format is easier to use as a command line argument.

See also

• JBrowseDev/Main