[maker-devel] Maker Snap annotation yields match_part

[Carson Holt]

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 <carsonhh at gmail.com> 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 <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 <http://gmod.org/wiki/Main_Page>
> 
> —Carson
> 
> 
>> On Aug 21, 2020, at 12:38 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> 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 <carsonhh at gmail.com <mailto: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 <mailto: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>
>>> 
>> 
>> -- 
>> 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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