[Gmod-ajax] jbrowse and the canonical gene

[James C. <ca...@gm...>]

Hi everyone,

Just before I get to my point, I want to say congratulations on
JBrowse.  I think it is the best genome browser I have seen by a long
way.

So I thought I would try out jbrowse with some GFF3 and to warm me up
I went straight to 'the canonical gene' from here:
http://www.sequenceontology.org/gff3.shtml

Now unfortunately, jbrowse doesn't render the CDSs correctly.  This is
because there are multiple lines with the same ID which correspond to
a spliced product that are shown as one giant CDS in jbrowse.
Changing the IDs to be different allows jbrowse to render it
correctly.

So looking further up the GFF3 definition:
"ID Indicates the name of the feature. IDs must be unique within the
scope of the GFF file."

Hmmm... so the canonical gene is wrong!  I suppose this should really
get flagged as a warning when the GFF is parsed rather than silently
merging features.

James