Actually, you may want to define all the three contigs you are using in your GFF file in the same way. -Ram


On May 15, 2012, at 9:56 PM, Podicheti, Ram wrote:

Hi Ashley,
Can you try updating the first line of your GFF file setting the ID and Name of the contig to the sequence ID?

For eg: 

C01_001 Genbank contig 1 4659 . + 1 ID=C01_001;Dbxref=taxon:1095103;Name=C01_001;

ID and Name define the SeqID which identifies the landmark you are trying to display.

Please let me know how it goes.

Cheers,

Ram


On May 15, 2012, at 9:35 PM, Ashley Lu wrote:

Hi everyone,
 
I am completely new to GBrowse, and trying tying  to get my head around this toll.
So I have a genbank file, and I used the bp_genbank2gff3.pl to convert it to a gff format.
and I have trouble displaying this gff file on webGBrowse.
 
I’ve use the ‘gff3-validator’ tool to check the format of the gff file, and nothing unusual.
Also I’ve noticed that when I tried to do a search using column 1 of the gff file, sometimes it appears as ‘landmark name not recognised’,
and sometimes it did manage to find the landmark by giving a message ‘The following 3 regions match your request’,  but either ways, no image is produced.
 
Can you please have a look at this gff file and see what might be causing trouble?
 
Thank you very mcuh
 
Ashley Lu
Research Associate
 
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