[Gmod-help] Chado - Apollo Tier Display

[Yap, Soon]

Hi Dave,

  I reallize I should have send the question to the Apollo list after i send the question to GMOD. Thanks!

  Regards,

SoonJoo,Yap 


-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
Sent: Wed 08/07/2009 19:36
To: Yap, Soon
Cc: GMOD Help Desk
Subject: Re: [Gmod-help] Chado - Apollo Tier Display
 
Hi SoonJoo,

I was going to recommend that you post this question to the Apollo
list, but I see you have already done this.  If you don't get an
answer there within a day or two, I'll try and stir things up.

Thanks,

Dave C

On Wed, Jul 8, 2009 at 2:48 PM, Yap, Soon<syap at jcvi.org> 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,
>
>
>
> SoonJoo,Yap



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