Hi Soon, Sounds like the data isn't getting loaded from the database. You'll need to make sure you add the proper types to your "chado-adapter.xml" that you're using. Take a look at the userguide:
http://apollo.berkeleybop.org/current/userguide.html#CustomizingChadoAdapter In particular you should look into the following elements: <genePredictionPrograms> <searchHitPrograms> <oneLevelAnnotTypes> <threeLevelAnnotTypes> in the <chadoInstance> element. Let me know if you have questions getting that set up. Cheers, Ed On Wed, 8 Jul 2009, Yap, Soon wrote:
Dear support, I’m trying to use Apollo for annotation purposes. I’ve setup the Chado database and was able to load in the fasta file into the database. Other then the fasta file, I was able to load some of the gene prediction gff file to the chado database in gff3 format with column no. 3 being CDS, gene, exon, mRNA, and cDNA_match. I’m able to use Artemis to connect to the database, and able to visualize the feature I loaded in. However, when I use Apollo to view the database, all of the above mention features cannot be seen on the Apollo, even I’ve tried to expand all the tiers. I know need to setup the tiers style to be able to view the features. Under the preferences, Type -> Tier, I’ve created a new tier profile with Visible, Labeled and Expanded option ticked. Under the drawing group, I’ve also created a new drawing group, and I’ve put in CDS, gene, exon, mRNA, and cDNA_match in the “Apply to following data types” window. I’ve save the tiers file, restart Apollo, but I’m still unable to see the features I’ve loaded in. Any guide to solve this problem is highly appreciated, thank you! Regards,
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