[maker-devel] non-redundant fasta and gff

[Carson Holt]

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