[Gmod-help] GBrowse 2 processed_transcript tracks
Scott Cain
scott at scottcain.net
Mon Sep 28 10:26:34 EDT 2009
Hello Wan Ting,
None of the built in aggregators work for you because you don't have
the right data types. If you had "transcript" features that were
parents to your exons, you would be able to use the transcript
aggregator. As the data stands, you need to write an aggregator
yourself to use your data. Something like:
aggregators = trans{exon}
would work, and then a track definition that uses it:
[Transcripts]
feature = trans
glyph = segments
...
Please read the sections in the tutorial about creating aggregators:
http://gmod.org/gbrowse-cgi/tutorial/dbgff/tutorial.html#custom_aggregators
Scott
On Mon, Sep 28, 2009 at 2:27 AM, POH Wan Ting <pohwat1 at gis.a-star.edu.sg> wrote:
> Hi Scott,
>
> I have tried all the aggregators and they do not work. Maybe I should illustrate my problem more clearly. I have attached 2 screens of the browser. When I set the region to chr1:740000..830000, the full gene of, say uc001abp.1 can be seen. The gene can be seen clearly with all the linkages between the spliced exons. But when I zoom in to chr1:761000..769000, where there are linkages but not exons, the linkages that can be seen in the first picture cannot be seen here. Hg18 UCSC Known Gene track is transcript and hg18 UCSC RefGene track is processed_transcript.
>
> The 2 other feature types in this data file are start_codon and CDS.
>
> | 3 | exon | hg18_knownGene |
> | 4 | start_codon | hg18_knownGene |
> | 5 | CDS | hg18_knownGene |
>
> Your help is very much appreciated.
>
> 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.
> ---------------------------------
> -----Original Message-----
> From: Scott Cain [mailto:scott at scottcain.net]
> Sent: Monday, September 28, 2009 11:18 AM
> To: POH Wan Ting
> Cc: help at gmod.org
> Subject: Re: [Gmod-help] GBrowse 2 processed_transcript tracks
>
> 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
>>
>> ---------------------------------
>> 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.
>> ---------------------------------
>> -----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
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
More information about the Gmod-help
mailing list