[maker-devel] ab-initio gene-prediction

[Carson Holt]

Is it possible that you just picked a contig that didn't have any pred_gff
entries for snap and augustus the first time?  The predictions you pass
through should be of type match/match_part and will have the source as
pred_gff:snap or pred_gff:augustus.  Could you check and let me know or
send me an example of entries from a contig you passed through and the
results you are seeing?

No. there is no priority given to one prediction over the other.  They are
choses based on evidence overlap similarity.

Thanks,
Carson




On 12-11-20 6:39 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:

>Hello,
>
>Just found that for Scaffold of larger size it does explicitly specify the
>prediction source.
>
>Thanks,
>Parul
>
>> Hello,
>>
>> I am running SNAP, Augustus and genemark(genemarkE results were
>>calculated
>> externally and gff3 file was provided to option pred_gff). However the
>> resulting gff3 source field does not mention if the prediction were
>> derived from  SNAP, Augustus or genemark. I have attached the
>> configuration file. Also is there any option where were could have
>> priority for SNAP predictions?
>>
>> Thanks and regards,
>> Parul Kudtarkar
>>
>> --
>> Scientific Programmer
>> Center for Computational Regulatory Genomics
>> Beckman Institute,
>> California Institute of Technology
>> http://www.spbase.org
>
>
>--
>Scientific Programmer
>Center for Computational Regulatory Genomics
>Beckman Institute,
>California Institute of Technology
>http://www.spbase.org
>
>
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