[maker-devel] Maker Snap annotation yields match_part

[Emmanuel Nnadi]

Thanks Carson

Please how do I assemble the match-part on the match parent? Any
special instruction on the maker control file?


On Fri, 21 Aug 2020 at 6:09 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
>
>
> --
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
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