[maker-devel] ab-initio gene-prediction

[Carson Holt]

They should show up as genemark or pred_gff:genemark.  Could you verify
that the input file from genemark indeed contained predictions that should
have been on this contig as not all contigs may have calls from genemark?

--Carson



On 12-11-26 2:21 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:

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