Maker Snap annotation yields match_part

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Maker Snap annotation yields match_part

Emmanuel Nnadi


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: 

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker Snap annotation yields match_part

Carson Holt-2
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 <[hidden email]> 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: 


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: 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 <[hidden email]> 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 <[hidden email]> 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: 



--
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

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker Snap annotation yields match_part

Carson Holt-2
If you want to try and do this programmatically, you can try libraries like the Gene Annotation Library (GAL) from the Sequence Ontology —> https://github.com/The-Sequence-Ontology/GAL

Or if you are looking for visualization or other manipulation you can try one of the GMOD tools —> http://gmod.org/wiki/Main_Page

—Carson


On Aug 21, 2020, at 12:38 PM, Emmanuel Nnadi <[hidden email]> wrote:

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 <[hidden email]> 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 <[hidden email]> 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: 



--
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


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker Snap annotation yields match_part

Carson Holt-2
Also, if you are just trying to see what the gene model of a match/match_part would have been, you can change maker_opts.ctl settings to keep all models (keep_pred=1) or pass in the models you want as match/match_part (Fred_gff=) and then let it be turned into an mRNA/exon/CDS feature.

match/match_part are reference features that let you see where the annotations came from.

—Carson

On Aug 21, 2020, at 12:47 PM, Carson Holt <[hidden email]> wrote:

If you want to try and do this programmatically, you can try libraries like the Gene Annotation Library (GAL) from the Sequence Ontology —> https://github.com/The-Sequence-Ontology/GAL

Or if you are looking for visualization or other manipulation you can try one of the GMOD tools —> http://gmod.org/wiki/Main_Page

—Carson


On Aug 21, 2020, at 12:38 PM, Emmanuel Nnadi <[hidden email]> wrote:

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 <[hidden email]> 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 <[hidden email]> 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: 



--
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



_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org