[maker-devel] NCBI feature table

[Michael Thon]

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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