[maker-devel] ab-initio gene-prediction

[Carson Holt]

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
>>>
>>>
>>>_______________________________________________
>>>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