[maker-devel] ab-initio gene-prediction

[Parul Kudtarkar]

Hello Carson,

Thanks for the feedback.Genemark was run outside maker and the resulting
gff3 file was provided as option to pred_gff. What would the source in the
gff3 of maker result state of the predictions where made from pred_gff?

Thanks and regards,
Parul Kudtarkar

> I see both augustus and snap derived predictions (match/match_part) with
> augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that
> were derived from these predictions.  There are no predictions from
> genemark.  Is that what you were expecting? If not could you specify how
> it varies.
>
> With respect to bootstrapping, it really depends how well trained your
> gene predictors are.  In general only one round of bootstrapping may be
> necessary after newly training a gene predictor.
>
> Thanks,
> Carson
>
>
>
> On 12-11-21 4:15 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:
>
>>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
>>>>
>>>>
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>>>>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
>
>
>


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