Hi Jen,

Many thanks for the reply. Sadly my programming is not up to anything like a 
gbk to gtf converter! The main reason I want one is that as a virologist this 
would be very useful since many viruses do not have a gtf file but do have 
genbank submissions. I know of a site that has some viruses listed together 
with GFF files but alas I cannot find a GFF to GTF converter - nightmare!!

I'll keep looking for one and if I find it I'll let you know.

Cheers
David


On 23 Mar 2011, at 18:02, Jennifer Jackson wrote:

> Hello David,
> 
> This is a great idea that the team has been considering adding, but nothing 
> immediate is planned. There are some external teams that are working on 
> outside development, and this is on their list, to.
> 
> If interested in what that project is doing, please see this thread:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004692.html
> 
> For now, if the data resides in a track at UCSC (many are, especially for 
> vertebrate genomes and it is updated daily), using the Table browser can 
> allow you to export the data in GTF and push to Galaxy with the "Get Data" 
> tool. Since some of the data can be large, using BX Main (our local UCSC 
> mirror) may be the best source.
> 
> To do this, navigate to the target genome and track (RefSeq under Gene 
> Predictions, others under Mrna & EST), and choose output format "GTF - gene 
> transfer format". Please note that the "gene_id" attribute in the 9th field 
> will not be populated with the gene name (will be same as transcript_id). 
> This is just how UCSC does it right now (on their list to get the full GTF 
> output set up in the TB, as far as we know). But, to get that info now, go 
> back in and reexport the same table data again as "all fields from selected 
> table" into Galaxy and the gene name will be in the data field named "name2". 
> The text manipulation tools can help to format the data.
> 
> A workflow would be a good option once you have the tool path worked out, so 
> that it can be reused without having to do it all again, for future similar 
> genbank datasets. You may even want to publish the workflow for others to 
> use, as it is very popular request, maybe add published page to explain how 
> to use/prep data for input.
> 
> Apologies for the current inconvenience, but hopefully this can get you going 
> until a more direct method is implemented directly in Galaxy main.
> 
> Great idea that many other users are also very interested in. Any 
> contributions (page, workflow) would be most welcomed. A tool that does the 
> extraction directly from Genbank would also be welcomed in the Tool Shed, if 
> you want to contribute.
> http://community.g2.bx.psu.edu/
> 
> Best,
> 
> Jen
> Galaxy team
> 
> 
> On 3/14/11 1:15 PM, David Matthews wrote:
>> Hi again,
>> 
>> Does anyone know of a genbank to gtf converter? I have heard such things 
>> exist but never found one...
>> 
>> Cheers
>> David
>> 
>> 
>> ___________________________________________________________
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> 
> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org


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