[Gmod-help] Re: [Gmod-gbrowse] multi-segmented feature looks fine at low power, but connecting lines between segments disappear when zoomed in
Scott Cain
cain.cshl at gmail.com
Mon Sep 15 16:02:43 EDT 2008
Shoot, that is what I was going to suggest you do. Could you send me
a sample of this data and the config file (and I appologize in advance
if you already did--I've been working on several different things at
once in the last week).
Scott
On Mon, Sep 15, 2008 at 3:53 PM, Bakir, Burcu <BBakir at hmgc.mcw.edu> wrote:
> Hi Scott and Dave,
>
> In addition to changing iD to ID in the database (fattribute table,
> fattribute_name field), as a second trial, I changed iD to ID in the
> gff3 file and then loaded into database with bp_load_gff.pl script. This
> approach didn't solve the problem either. Do you have any other
> suggestions?
>
> Thanks,
>
> Burcu
>
> -----Original Message-----
> From: Bakir, Burcu
> Sent: Thursday, September 11, 2008 3:18 PM
> To: 'Scott Cain'; 'help at gmod.org'
> Cc: 'gmod-gbrowse at lists.sourceforge.net'
> Subject: RE: [Gmod-gbrowse] multi-segmented feature looks fine at low
> power, but connecting lines between segments disappear when zoomed in
>
> Hi Scott and Dave,
>
> Unfortunately changing iD to ID didn't solve my problem. I did the
> change in database (fattribute table, fattribute_name field).
>
> I also checked my gff3 files that bp_genbank2gff3.pl script produced out
> of rn_ref_chr1.gbk file. ID tag is used for region type (ID=NW_047334).
> All other types have iD tag. I thought the script does this on purpose.
> Here is a few other lines from my gff3 file. Do you have any other
> suggestions?
>
> ##gff-version 3
> Chr10 GenBank region 13176264 58337323 . .
> . ID=NW_047334
> Chr10 GenBank contig 13176264 58337323 . +
> . iD=GenBank:contig:NW_047334:1:45161060;mol_type=genomic
> DNA;db_xref=taxon:10116;strain=BN/SsNHsdMCW;chromosome=10;organism=Rattu
> s norvegicus
> Chr10 GenBank gap 13185425 13185759 . +
> . iD=GenBank:gap:NW_047334:9162:9496;estimated_length=335
> Chr10 GenBank gene 13183520 13186891 . +
> . iD=Sbp;db_xref=GeneID:25540,RGD:3623;gene=Sbp;note=Derived by
> automated computational analysis using gene prediction method:
> BestRefseq. Supporting evidence includes similarity to: 1 mRNA
>
> Thanks,
>
> Burcu
>
> -----Original Message-----
> From: Scott Cain [mailto:cain.cshl at gmail.com]
> Sent: Thursday, September 11, 2008 8:30 AM
> To: help at gmod.org
> Cc: Bakir, Burcu; gmod-gbrowse at lists.sourceforge.net
> Subject: Re: [Gmod-gbrowse] multi-segmented feature looks fine at low
> power, but connecting lines between segments disappear when zoomed in
>
> Good call Dave! I didn't see that, but it would certainly cause what
> Burcu is seeing.
>
> Scott
>
> On Thu, Sep 11, 2008 at 9:23 AM, Dave Clements, GMOD Help Desk
> <gmodhelp at googlemail.com> wrote:
>> Hi Burcu,
>>
>> I just started looking at this. So far only one thing stands out. In
>> the GFF file, column 9 for the gene and mRNA lines, the "iD" tag
>> should be "ID" instead. Column 9 tag names are case sensitive.
>>
>> I don't know if this would cause the problem you are seeing, but it
>> will cause problems. I'll keep investigating. Please let me know
>> what difference this change makes.
>>
>> Thanks,
>> Dave C
>> GMOD Help Desk
>>
>> On Mon, Sep 8, 2008 at 9:37 PM, Bakir, Burcu <BBakir at hmgc.mcw.edu>
> wrote:
>>> Hi,
>>>
>>>
>>>
>>> I have a multi-segmented feature (such as a multi-exon transcript).
> It looks
>>> fine at low power, but when I zoom in the connecting lines between
> segments
>>> disappear. I have seen the same problem at GMOD FAQ. It suggests:
> "For
>>> transcripts, use the "processed_transcript" aggregator and create
> features
>>> with a main part of "mRNA" and subparts of "CDS", "exon", and/or
> various
>>> types of UTRs." Is the solution suggested above valid for gff2 files
> but
>>> not for gff3 files? I use gff3 file produced by bp_genbank2gff3.pl
> script.
>>> And this solution didn't work out for me. What else should I do?
>>>
>>>
>>>
>>> I have defined an aggregator as:
>>>
>>> EntrezGene{CDS,exon/mRNA}
>>>
>>> At the aggregators section of configuration file I have used
>>> processed_transcript as a glyph. I ended up having only curved lines
> for
>>> mRNA. Later when I define aggregator as:
>>>
>>> aggregators = EntrezGene{CDS,exon,gene}
>>>
>>> I ended up having nice picture at low power, but when I zoom in the
>>> connecting lines between segments disappear. Here is a sample of gff3
> file
>>> for LOC686032 gene:
>>>
>>>
>>>
>>> Chr1 GenBank gene 20302435 20339168 . +
>>> .
> iD=LOC686032;db_xref=GeneID:686032;gene=LOC686032;note=Derived by
>>> automated computational analysis using gene prediction method:
> GNOMON.
>>> Supporting evidence includes similarity to: 4 ESTs
>>>
>>> Chr1 GenBank mRNA 20302435 20339168 . +
>>> .
>>>
> iD=LOC686032.t01;Parent=LOC686032;db_xref=GI:109457633,GeneID:686032;gen
> e=LOC686032;product=hypothetical
>>> protein LOC686032;transcript_id=XM_001066267.1;note=Derived by
> automated
>>> computational analysis using gene prediction method: GNOMON.
> Supporting
>>> evidence includes similarity to: 4 ESTs
>>>
>>> Chr1 GenBank CDS 20302507 20302633 . +
>>> .
>>>
> Parent=LOC686032.t01;db_xref=GI:109457634,GeneID:686032;codon_start=1;pr
> otein_id=XP_001066267.1;gene=LOC686032;product=hypothetical
>>> protein
>>>
>>> Chr1 GenBank CDS 20338800 20338879 . +
>>> .
>>>
> Parent=LOC686032.t01;db_xref=GI:109457634,GeneID:686032;codon_start=1;pr
> otein_id=XP_001066267.1;gene=LOC686032;product=hypothetical
>>> protein
>>>
>>> Chr1 GenBank exon 20302435 20302633 . +
>>> . Parent=LOC686032.t01;gene=LOC686032
>>>
>>> Chr1 GenBank exon 20338800 20339168 . +
>>> . Parent=LOC686032.t01;gene=LOC686032
>>>
>>>
>>>
>>> Here is part of my conf file:
>>>
>>> aggregators = transcript
>>>
>>> EntrezGene{CDS,exon,gene}
>>>
>>>
>>>
>>> [EntrezGene]
>>>
>>> category = ENTREZ
>>>
>>> feature = EntrezGene:GenBank
>>>
>>> glyph = processed_transcript
>>>
>>> fgcolor = turquoise
>>>
>>> bgcolor = turquoise
>>>
>>> height = 10
>>>
>>> key = Entrez Genes
>>>
>>>
>>>
>>> Here is my workflow in order to create a new gene track using GenBank
> files:
>>>
>>> I started with rn_ref_chr1.gbk file.
>>> Get gff3 file using bp_genbank2gff3.pl script.
>>> Load into MySQL database with bp_load_gff.pl script.
>>> Edit configuration file for visualizing transcripts.
>>>
>>>
>>>
>>> First 3 steps work fine but I think I need to change something with
> the
>>> configuration file. I have tried several other glyph vs aggregator
>>> combinations but none of them worked out.
>>>
>>>
>>>
>>> Thanks for your suggestions.
>>>
>>>
>>>
>>> Burcu Bakir-Gungor
>>>
>>> Programmer Analyst
>>>
>>> Medical College of Wisconsin
>>>
>>> Human Molecular Genetics Center
>>>
>>> Bioinformatics Program
>>>
>>> Rat Genome Database Project
>>>
>>> Email: bbakir at mcw.edu
>>>
>>>
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>>
>>
>>
>> --
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>>
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>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. cain.cshl at gmail.com
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Cold Spring Harbor Laboratory
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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