[maker-devel] NCBI feature table

[Carson Holt]

Yes.  The non-web version of apollo can open GFF3 and then save to table
format —> http://sourceforge.net/projects/gmod/files/Apollo/

I’ve also attached a script made by a lab member that can convert MAKER
derived GFF3 gene entries into raw table format, and I’ve CC’d the scripts
author (Michael Campbell) incase you have any questions.

Thanks,
Carson


On 2/7/14, 7:14 AM, "Michael Thon" <mike.thon at gmail.com> wrote:

>Hi Ian -
>
>We've been struggling with this too and I started developing a script to
>convert the maker gff into ncbi's .tbl format.  However we found that
>some of the gene models required manual editing so what we do is import
>the gff into a commercial application called Geneious where we do the
>edits.  From there we export the data in genbank format and then convert
>it to .tbl format with a script. Our submission just passed the automated
>checks and we're waiting for the manual review. Probably none of my code
>will help you, and in any case its kind of a mess.  The only advice I can
>offer is to say that you'll probably need some manual editing in your
>workflow, if not Apollo, then some other app.  In that case you'll need
>to convert the output of that app into .tbl format.
>
>> On Feb 7, 2014, at 2:29 PM, UMD Bioinformatics
>><bioinformatics.umd at gmail.com> wrote:
>> 
>> Hello Maker Developers,
>> 
>> I have used this software with great success and I continue to look to
>>it going forward. However, as I’m getting ready to submit my annotations
>>to NCBI with the genomes I haven’t found a straightforward method of
>>turning the MAKER produced GFF files into a NCBI feature table. What is
>>the process for creating this table? It seem that the format NCBI is
>>looking for is unique and I haven’t uncovered any scripts or tools to
>>assist in the creation of this table from my annotation files. If anyone
>>has any insight on this issue it would be greatly appreciated.
>> 
>> Cheers
>> Ian
>> 
>> 
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