[Gmod-help] Re: [Gmod-gbrowse] multi-segmented feature looks fine at low power, but connecting lines between segments disappear when zoomed in

[Scott Cain]

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;gene=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;protein_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;protein_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
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory