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Re: The landmark named contig18281:1..500 is not recognized

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Re: The landmark named contig18281:1..500 is not recognized

Ram Podicheti-2
Hi Amol,
Besides the gene, mRNA and CDS you will have to add a separate GFF3 line for each of the SeqIDs, in your GFF3 file these are all the contigs. The first step to do this would be obtaining the sequence length for each contig in the gff3 file. You can then add an additional line in your gff3 file for each contig as a contig definition. For eg: assume contig18281 has a length of 10,000 and contig18283 has a length of 15,000. You can define these two contigs:

contig18281        JGI      contig      1      10000     .        .        .          ID=contig18281;Name=contig18281
contig18283        JGI      contig      1      15000     .        .        .          ID=contig18283;Name=contig18283


Please note that each line has 9 columns that are tab separated. You can get more information on the gff3 format from here: http://www.sequenceontology.org/gff3.shtml.

Please let me know if you have more issues.

Cheers,

Ram
 


On Oct 19, 2012, at 9:59 AM, Amol Kolte wrote:

> Hello,
> I am trying to configure a gff3 file using WebGbrowse 2.0 and viewing online with Gbrowse2.0. But, I am constantly getting an error saying "The landmark named contig18281:1..500 is not recognized", although, this contig annotation is present in the .gff3 file.
> Similarly, all other contigs are not getting recognized as well.
>
> I have attached a sample file containing first 50 lines of the original file. Could you please tell me the problem.
>
> Regards,
> Amol  
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Re: The landmark named contig18281:1..500 is not recognized

Ram Podicheti-2
Amol,
WebGBrowse is meant for very basic GBrowse configuration without actually having to edit the configuration file. It cannot handle features like plugins, relational databases, wiggle or bigwig or SAM datasets. For these advanced features you need to modify your conf file manually. For details on how to do this , you can refer to the GBrowse HOWTOs and GBrowse administration tutorials.


You may also want to post in the GBrowse mailing list too.

cheers,

Ram


On Nov 5, 2012, at 1:49 AM, Amol Kolte wrote:

Hello Again Ram,
I was wondering whether if it is possible to configure certain plugins such as Blat, PrimerDesigner, GeneFinder and OligoFinder using WebGbrowse. I have installed the required executables for these plugins but I could not integrate them into Gbrowse (that requires modifying the config files). Also, I am not finding the perldocs for these modules very straightforward. Could you please tell me what can be done about it?

Regards,
Amol

On Sat, Oct 20, 2012 at 12:46 PM, Amol Kolte <[hidden email]> wrote:
Hi Ram,
I missed the obvious. Thank you for pointing that out. It was a nice explanation.


Regards,
Amol.



On Fri, Oct 19, 2012 at 8:50 PM, Podicheti, Ram <[hidden email]> wrote:
Hi Amol,
Besides the gene, mRNA and CDS you will have to add a separate GFF3 line for each of the SeqIDs, in your GFF3 file these are all the contigs. The first step to do this would be obtaining the sequence length for each contig in the gff3 file. You can then add an additional line in your gff3 file for each contig as a contig definition. For eg: assume contig18281 has a length of 10,000 and contig18283 has a length of 15,000. You can define these two contigs:

contig18281        JGI      contig      1      10000     .        .        .          ID=contig18281;Name=contig18281
contig18283        JGI      contig      1      15000     .        .        .          ID=contig18283;Name=contig18283


Please note that each line has 9 columns that are tab separated. You can get more information on the gff3 format from here: http://www.sequenceontology.org/gff3.shtml.

Please let me know if you have more issues.

Cheers,

Ram



On Oct 19, 2012, at 9:59 AM, Amol Kolte wrote:

> Hello,
> I am trying to configure a gff3 file using WebGbrowse 2.0 and viewing online with Gbrowse2.0. But, I am constantly getting an error saying "The landmark named contig18281:1..500 is not recognized", although, this contig annotation is present in the .gff3 file.
> Similarly, all other contigs are not getting recognized as well.
>
> I have attached a sample file containing first 50 lines of the original file. Could you please tell me the problem.
>
> Regards,
> Amol
> <send>------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________
> Gmod-webgbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse





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