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I'm trying to load gff (version 3) into Artemis for the first time (I've 
previously had good success loading data from GenBank files), and I'm having 
trouble displaying mRNA and CDS features. I'm using a test gff file containing 
1 gene. The feature entries in the gff are:

##gff-version 3
contig_1574 .  contig   1  105753   .  .  .  ID=contig_1574;Name=contig_1574;
contig_1574 maker mRNA  73760 75490 .  +  .  ID=m1;Name=m1;
contig_1574 maker exon  73760 73887 3.73  +  .  ID=m1:exon:1919;Parent=m1;
contig_1574 maker exon  73968 75490 33.33 +  .  ID=m1:exon:1920;Parent=m1;
contig_1574 maker CDS   73825 73887 0  +  0  ID=m1:cds:1864;Parent=m1;
contig_1574 maker CDS   73968 74417 0  +  0  ID=m1:cds:1865;Parent=m1;

The mRNA feature isn't displayed in the Overview/DNA views at all, and the 
feature key "mRNA" is greyed out in the Feature List. The individual CDS/exon 
features are displayed, but they aren't linked in the Overview and DNA views 
(whereas when I loaded from GenBank in the past, I see CDSs within a single 
gene linked by a line). I assumed the "Parent" qualifier in exon/CDS entries 
would result in linking multipart features.

The only message in the log is " 30 Mar 09:35 - BAM & VCF not visible." I'm 
running v13 via WebStart. If anyone would like the entire gff (including the 
contig fasta sequence) then please email me.

Any ideas on what I'm doing wrong?

Thanks (:

Anar Khan
T +64 3 489 9154
E anar.k...@agresearch.co.nz

AgResearch Limited
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
T  +64 3 489 3809   F  +64 3 489 3739  www.agresearch.co.nz

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