[Gmod-help] GBrowse 2 processed_transcript tracks

[Scott Cain]

Hi Wan Ting,

Is there an mRNA or other transcript type feature that is tying them together?

Please take a look at the section of the tutorial dealing with aggregators:

  http://gmod.org/gbrowse-cgi/tutorial/dbgff/tutorial.html#aggregators

You may want to use the "transcript" aggregator since you have exons.

Scott


On Sun, Sep 27, 2009 at 9:42 PM, POH Wan Ting <pohwat1 at gis.a-star.edu.sg> wrote:
> 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
>
>
>
>
>



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