NCBI feature table

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NCBI feature table

UMD Bioinformatics
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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Re: 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 <[hidden email]> 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
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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Re: NCBI feature table

Carson Hinton 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" <[hidden email]> 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
>><[hidden email]> 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
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> [hidden email]
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>_______________________________________________
>maker-devel mailing list
>[hidden email]
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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gff32table (10K) Download Attachment
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Re: NCBI feature table

Brian Hall
In reply to this post by UMD Bioinformatics
Hi Ian,

My colleagues are also working on preparing a genome for submission to
the NCBI. The software we are developing for this task is still a work
in progress, but you are welcome to give it a try:

https://github.com/tedsta/GAG

It's a console-based application and it requires Python 2.6. Its
strength is in filtering and modifying large segments of the genome at
once -- where Apollo is good for removing a few erroneous exons, we are
dealing with lists of dozens or more. This program seeks to make such
changes as painless as possible.

My advice is to try the simplest gff3-to-tbl script you can find and
then run tbl2asn. If it works out okay, great! If you get a massive
error report, get in touch and we'll help you out if we can :)

--Brian

On 02/07/2014 05:16 AM, [hidden email] wrote:

> Date: Fri, 7 Feb 2014 08:29:27 -0500
> From: UMD Bioinformatics <[hidden email]>
> To: [hidden email]
> Subject: [maker-devel] NCBI feature table
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=windows-1252
>
> 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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