[maker-devel] non-redundant fasta and gff

[Carson Holt]

Please see the documentation wiki for explanations of how to read and use
MAEKR's output.

http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_
GMOD_Online_Training_2014#MAKER.27s_Output

Thanks,
Carson



On 8/27/14, 9:57 AM, "Carson Holt" <carsonhh at gmail.com> wrote:

>The fasta files created for augustus, snap, etc. are only for reference
>purposes.  They are the raw ab initio prediction produced by these
>algorithms ran by themselves (they are match/match_part features in the
>GFF3 file).  The file you want is the maker.transcripts.fasta and
>maker.proteins.fasta files.  They contain the non-redundant final
>annotations.  They are the same ones that are marked as gene/mRNA/exon/CDS
>features in the GFF3 file.
>
>--Carson
>
>
>On 8/27/14, 9:52 AM, "Borhan, Hossein" <Hossein.Borhan at AGR.GC.CA> wrote:
>
>>Hi
>>
>>
>>Is there a way to produce a fasta file and gff for a set of non-redundant
>>genes predicted by the Maker software. Fasta-merge and gff-merge generate
>>a file that has  different prediction (e.g generated by Augustus,
>>GeneMark etc. ) for the same gene sac as as individual genes.
>>
>>
>>
>>Regards
>>
>>
>>Hossein
>>
>>
>>
>>
>>
>>
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>