ggb 1.71b using DAS server for the fasta sequences
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ggb 1.71b using DAS server for the fasta sequences
by Marc Wessner
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Hi,
I have to install many private genome browsers that display specific annotations on the human genome. I intend to configure a DAS server that could provide all the human common tracks for all my genome browsers, so I don't have to copy the whole genome fasta files and mRNA tracks data etc... several times. First of all, am I right or the fasta files have to be present in each browser database ? In a browser that shall use the DAS server (but doesn't yet), I have only loaded a few gff files : chromosome.gff, cytobands.gff and the annotations. Without the fasta files, when I try this genome browser alone, I get an error message that says:"chr?start:end reference is unknown!" (what ever the figures may be) Am I missing something ? I am using this documentation: http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS Shall I look anywhere else ? Where could I find an explanation of how the region is defined: - Is chromosome.gff not enough to display the annotations for a given region (I am not talking about bases or GC%) ? - Are fasta file madatory for such a purpose ? - Can the fasta sequences be part of what is gotten from the DAS in order (I hope so)? Thanks for your hints, Best regards Marc ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: ggb 1.71b using DAS server for the fasta sequences
by Dave Clements, GMOD Help Desk-2
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Hi Marc,
I'm not an experienced DAS person, but I might be able to shed some light on the error message. I believe the "chr?start:end reference is unknown!" error message is the result of not defining the whole chromosome somewhere. From the tutorial (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#data_file): --- It is very important to have a full-length entry (such as the one for ctgA) for each reference sequence mentioned in the first column of the GFF3 file. However, the reference sequence can have any source and type you choose. Commonly used types are "clone", "chromosome" and "contig." --- I *think* you need to define the overall chromosome in a local database. Does anyone else have suggestions? Thanks, Dave C. On Thu, Nov 5, 2009 at 8:57 AM, Marc Wessner <mwessner@...> wrote: > Hi, > > I have to install many private genome browsers that display specific > annotations on the human genome. > > I intend to configure a DAS server that could provide all the human > common tracks for all my genome browsers, so I don't have to copy the > whole genome fasta files and mRNA tracks data etc... several times. > First of all, am I right or the fasta files have to be present in each > browser database ? > > In a browser that shall use the DAS server (but doesn't yet), I have > only loaded a few gff files : chromosome.gff, cytobands.gff and the > annotations. > Without the fasta files, when I try this genome browser alone, I get an > error message that says:"chr?start:end reference is unknown!" (what ever > the figures may be) > > Am I missing something ? > I am using this documentation: > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS > Shall I look anywhere else ? > > Where could I find an explanation of how the region is defined: > - Is chromosome.gff not enough to display the annotations for a given > region (I am not talking about bases or GC%) ? > - Are fasta file madatory for such a purpose ? > - Can the fasta sequences be part of what is gotten from the DAS in > order (I hope so)? > > Thanks for your hints, > > Best regards > > Marc > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Please keep responses on the list! http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: ggb 1.71b using DAS server for the fasta sequences
by Scott Cain-4
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To add to this, and answer one of your other questions: you do not
absolutely need to have the dna sequences themselves to make gbrowse work: all you really need is a gff file that describes the features. You only need the dna sequence if you want to use the dna/gc content glyph or provide translations either for the translation glyph or in the cds glyph. Scott On Mon, Nov 9, 2009 at 5:54 PM, Dave Clements, GMOD Help Desk <help@...> wrote: > Hi Marc, > > I'm not an experienced DAS person, but I might be able to shed some > light on the error message. I believe the "chr?start:end reference is > unknown!" error message is the result of not defining the whole > chromosome somewhere. From the tutorial > (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#data_file): > > --- > It is very important to have a full-length entry (such as the one for > ctgA) for each reference sequence mentioned in the first column of the > GFF3 file. However, the reference sequence can have any source and > type you choose. Commonly used types are "clone", "chromosome" and > "contig." > --- > > I *think* you need to define the overall chromosome in a local database. > > Does anyone else have suggestions? > > Thanks, > > Dave C. > > > On Thu, Nov 5, 2009 at 8:57 AM, Marc Wessner <mwessner@...> wrote: >> Hi, >> >> I have to install many private genome browsers that display specific >> annotations on the human genome. >> >> I intend to configure a DAS server that could provide all the human >> common tracks for all my genome browsers, so I don't have to copy the >> whole genome fasta files and mRNA tracks data etc... several times. >> First of all, am I right or the fasta files have to be present in each >> browser database ? >> >> In a browser that shall use the DAS server (but doesn't yet), I have >> only loaded a few gff files : chromosome.gff, cytobands.gff and the >> annotations. >> Without the fasta files, when I try this genome browser alone, I get an >> error message that says:"chr?start:end reference is unknown!" (what ever >> the figures may be) >> >> Am I missing something ? >> I am using this documentation: >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS >> Shall I look anywhere else ? >> >> Where could I find an explanation of how the region is defined: >> - Is chromosome.gff not enough to display the annotations for a given >> region (I am not talking about bases or GC%) ? >> - Are fasta file madatory for such a purpose ? >> - Can the fasta sequences be part of what is gotten from the DAS in >> order (I hope so)? >> >> Thanks for your hints, >> >> Best regards >> >> Marc >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > > -- > Please keep responses on the list! > http://gmod.org/wiki/January_2010_GMOD_Meeting > http://gmod.org/wiki/GMOD_News > Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: ggb 1.71b using DAS server for the fasta sequences
by Lincoln Stein-3
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Hi Marc,
Each server will need a database that provides the names of the chromosomes and their lengths. This can be a flat GFF file, or any of the adapters that GBrowse supports. You do not need to provide the full FASTA file with the sequence unless the browser needs to display the sequence for GC content, stop sites, etc. Lincoln On Thu, Nov 5, 2009 at 11:57 AM, Marc Wessner <mwessner@...> wrote: Hi, -- 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@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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