[Gmod-help] GBrowse 2 processed_transcript tracks
Lincoln Stein
lincoln.stein at gmail.com
Mon Sep 28 11:30:18 EDT 2009
Hi,
It won't work unless you tie the exons together with an mRNA feature. I
think the UCSC converter tool does this for you.
Lincoln
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
>
--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20090928/c4050d29/attachment.html>
More information about the Gmod-help
mailing list