[Gmod-help] RE: [Gmod-gbrowse] multi-segmented feature looks fine at low power, but connecting lines between segments disappear when zoomed in
Bakir, Burcu
BBakir at hmgc.mcw.edu
Mon Sep 15 15:53:28 EDT 2008
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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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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