Difference between revisions of "JBrowseDev/The SubfeatureClasses Option"
From GMOD
RSCummings (Talk | contribs) m (→See also) |
RSCummings (Talk | contribs) m (→See also) |
||
(One intermediate revision by the same user not shown) | |||
Line 11: | Line 11: | ||
=See also= | =See also= | ||
− | * [[JBrowseDev | + | * [[JBrowseDev/General Usage | General Usage Notes]] |
[[Category:JBrowse]] | [[Category:JBrowse]] |
Latest revision as of 17:47, 29 July 2011
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.