genome annotation from Drosophila melanogaster r5.19
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genome annotation from Drosophila melanogaster r5.19
by vipin.ts
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Hello all,
I am trying to display the genome annotation from Drosophila melanogaster r5.19 release. Here the display is not coming through the browser. Please find the attached file with this.(It is screen shot for my gbrowse dmel display) Back end data storage MySQL BioPerl 1.6.0 Gbrowse 1.70 Data adaptor Bio::DB::SeqFeature::Store -- Vipin T S ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: genome annotation from Drosophila melanogaster r5.19
by Dave Clements, GMOD Help Desk
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Hi Vipin,
Based on your subsequent post to the list, you have already this problem out. For future reference, in general, when GBrowse is giving you empty or nearly empty results, the best place to look for hints on the problem is the Apache error log. Dave C. On Thu, Sep 17, 2009 at 9:06 AM, Vipin TS <vipin.ts@...> wrote: > Hello all, > > I am trying to display the genome annotation from Drosophila melanogaster > r5.19 release. Here the display is not coming through the browser. Please > find the attached file with this.(It is screen shot for my gbrowse dmel > display) > > Back end data storage MySQL > BioPerl 1.6.0 > Gbrowse 1.70 > Data adaptor Bio::DB::SeqFeature::Store > > -- > Vipin T S > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: genome annotation from Drosophila melanogaster r5.19
by vipin.ts
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Hi Dave,
I cannot see any relevant errors in apache error log. 2009/9/18 Dave Clements, GMOD Help Desk <gmodhelp@...> Hi Vipin, -- Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: genome annotation from Drosophila melanogaster r5.19
by Scott Cain-4
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Hi Vipin,
There was a problem with the FlyBase GFF3 that caused some strange problems, but I don't remember exactly what they were. Josh, does this sound familiar? Thanks, Scott On Sep 18, 2009, at 3:25 PM, Vipin TS wrote: > Hi Dave, > > I cannot see any relevant errors in apache error log. > > 2009/9/18 Dave Clements, GMOD Help Desk <gmodhelp@...> > Hi Vipin, > > Based on your subsequent post to the list, you have already this > problem out. > > For future reference, in general, when GBrowse is giving you empty or > nearly empty results, the best place to look for hints on the problem > is the Apache error log. > > Dave C. > > On Thu, Sep 17, 2009 at 9:06 AM, Vipin TS <vipin.ts@...> wrote: > > Hello all, > > > > I am trying to display the genome annotation from Drosophila > melanogaster > > r5.19 release. Here the display is not coming through the browser. > Please > > find the attached file with this.(It is screen shot for my gbrowse > dmel > > display) > > > > Back end data storage MySQL > > BioPerl 1.6.0 > > Gbrowse 1.70 > > Data adaptor Bio::DB::SeqFeature::Store > > > > -- > > Vipin T S > > > > > > > ------------------------------------------------------------------------------ > > Come build with us! The BlackBerry® Developer Conference in > SF, CA > > is the only developer event you need to attend this year. > Jumpstart your > > developing skills, take BlackBerry mobile applications to market > and stay > > ahead of the curve. Join us from November 9-12, 2009. Register > now! > > http://p.sf.net/sfu/devconf > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmod-gbrowse@... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > > > > -- > Vipin T S > Friedrich Miescher Laboratory of the Max Planck Society > Spemannstrasse 39, 72076 > Tuebingen, Germany > Tel:+49 7071 601 824 > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf_______________________________________________ > 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 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: genome annotation from Drosophila melanogaster r5.19
by Josh Goodman
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Yep that is the one. I added a note to our GFF README about it for our more recent release.
ftp://flybase.org/genomes/dmel/current/gff/README You can either remove the feature lines of type 'orthologous_to' or remove the Target tag from all of these feature lines. Cheers, Josh Scott Cain wrote: > Hi Vipin, > > There was a problem with the FlyBase GFF3 that caused some strange > problems, but I don't remember exactly what they were. > > Josh, does this sound familiar? > > Thanks, > Scott > > > On Sep 18, 2009, at 3:25 PM, Vipin TS wrote: > >> Hi Dave, >> >> I cannot see any relevant errors in apache error log. >> >> 2009/9/18 Dave Clements, GMOD Help Desk <gmodhelp@...> >> Hi Vipin, >> >> Based on your subsequent post to the list, you have already this >> problem out. >> >> For future reference, in general, when GBrowse is giving you empty or >> nearly empty results, the best place to look for hints on the problem >> is the Apache error log. >> >> Dave C. >> >> On Thu, Sep 17, 2009 at 9:06 AM, Vipin TS <vipin.ts@...> wrote: >> > Hello all, >> > >> > I am trying to display the genome annotation from Drosophila >> melanogaster >> > r5.19 release. Here the display is not coming through the browser. >> Please >> > find the attached file with this.(It is screen shot for my gbrowse dmel >> > display) >> > >> > Back end data storage MySQL >> > BioPerl 1.6.0 >> > Gbrowse 1.70 >> > Data adaptor Bio::DB::SeqFeature::Store >> > >> > -- >> > Vipin T S >> > >> > >> > >> ------------------------------------------------------------------------------ >> >> > Come build with us! The BlackBerry® Developer Conference in SF, CA >> > is the only developer event you need to attend this year. Jumpstart >> your >> > developing skills, take BlackBerry mobile applications to market and >> stay >> > ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> > http://p.sf.net/sfu/devconf >> > _______________________________________________ >> > Gmod-gbrowse mailing list >> > Gmod-gbrowse@... >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > >> > >> >> >> >> -- >> * Please keep responses on the list! >> * Was this helpful? Let us know at >> http://gmod.org/wiki/Help_Desk_Feedback >> >> >> >> -- >> Vipin T S >> Friedrich Miescher Laboratory of the Max Planck Society >> Spemannstrasse 39, 72076 >> Tuebingen, Germany >> Tel:+49 7071 601 824 >> ------------------------------------------------------------------------------ >> >> Come build with us! The BlackBerry® Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> http://p.sf.net/sfu/devconf_______________________________________________ >> >> 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 > > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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