[maker-devel] ab-initio gene-prediction

[Parul Kudtarkar]

Dear Carson,

That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb
which is very small). I have attached a Scaffold of 1.5kb with no
predictions and another Scaffold of 28kb. It is of course expected that we
would not get any gene-prediction for small size Scaffolds.

For next maker run would you recommend bootstrap to reduce false positives?

Thanks and regards,
Parul Kudtarkar

> 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
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>


--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org
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