[Gmod-help] GBrowse 2 processed_transcript tracks

[POH Wan Ting]

Hi Scott,

Thank you for your reply. I am using db_adaptor    = Bio::DB::GFF. And
the database is downloaded from ucsc known genes in gtf format as below:

chr1    hg18_knownGene  exon    1116    2090    0.000000        +
.       gene_id "uc001aaa.2"; transcript_id "uc001aaa.2"; 
chr1    hg18_knownGene  exon    2476    2584    0.000000        +
.       gene_id "uc001aaa.2"; transcript_id "uc001aaa.2"; 
chr1    hg18_knownGene  exon    3084    4121    0.000000        +
.       gene_id "uc001aaa.2"; transcript_id "uc001aaa.2"; 
chr1    hg18_knownGene  exon    1116    2090    0.000000        +
.       gene_id "uc009vip.1"; transcript_id "uc009vip.1"; 
chr1    hg18_knownGene  exon    2476    4272    0.000000        +
.       gene_id "uc009vip.1"; transcript_id "uc009vip.1"; 
chr1    hg18_knownGene  exon    4269    4692    0.000000        -
.       gene_id "uc009vis.1"; transcript_id "uc009vis.1"; 
chr1    hg18_knownGene  exon    4833    4901    0.000000        -
.       gene_id "uc009vis.1"; transcript_id "uc009vis.1"; 
chr1    hg18_knownGene  exon    5659    5805    0.000000        -
.       gene_id "uc009vis.1"; transcript_id "uc009vis.1"; 
chr1    hg18_knownGene  exon    6470    6628    0.000000        -
.       gene_id "uc009vis.1"; transcript_id "uc009vis.1";

Best Regards,
Wan Ting
 
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-----Original Message-----
From: Scott Cain [mailto:scott at scottcain.net] 
Sent: Friday, September 25, 2009 9:23 PM
To: POH Wan Ting
Cc: help at gmod.org
Subject: Re: [Gmod-help] GBrowse 2 processed_transcript tracks

Hi Wan Ting,

When a problem like that happens, it is usually an aggregator issue.   
Which data adaptor are you using (Bio::DB::GFF,  
Bio::DB::SeqFeature::Store or something else)?

Scott


On Sep 25, 2009, at 2:06 AM, POH Wan Ting wrote:

> Hi,
>
> I noticed for the processed transcript tracks, the intron regions  
> will not be shown when zoomed in.
> For example, there is a gene  uc009vip.1 at chr1:1116..4272 when I  
> set the browser to this range, I can see the full gene. But when I  
> zoom into an intron region, say chr1:2160..2370, the gene will not  
> be shown. Is there a way to display the gene even if it's in the  
> intron region?
>
> Thanks in advance for your help!
>
> Best Regards,
> Wan Ting
>
> ---------------------------------
> This email is confidential and may be privileged. If you are not the  
> intended recipient, please delete it and notify us immediately.
> Please do not copy or use it for any purpose, or disclose its  
> content to any other person. Thank you.
> ---------------------------------

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research