[maker-devel] Maker Snap annotation yields match_part

[Carson Holt]

If you just want a count you can grep for match with tabs at either side —> grep -P “\tmatch\t” file.gff

If you want the model, you need to assemble the match parts onto the match parent.

—Carson


> On Jul 26, 2020, at 11:31 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> 
> Hello,
> I am annotating my genome using SNAP after running SNAP twice my GFF has quite a number of match_part. How can I get an actual match?
> 
> 
> 
> ilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 890 1003 +;Gap=M114
> contig_844_pilon_pilon_pilon    snap_masked     match_part      66719   66729   8.644   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2866471:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1004 1014 +;Gap=M11
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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