[maker-devel] AED score

[Parul Kudtarkar]

Thanks for quick response Daniel, I'll do it through maker.

> Hi Parul,
>
> I think the way you described (with the maker_opts.ctl file) is how you
> want to proceed. You still need to give the genome too.
>
> Daniel
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ________________________________________
> From: maker-devel-bounces at yandell-lab.org
> [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar
> [parulk at caltech.edu]
> Sent: Tuesday, November 27, 2012 3:41 PM
> To: Parul Kudtarkar
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] AED score
>
> Also, are there any other parameters that are required when filtering
> based on AED score?
>
>> Hello Carson,
>>
>> Just to confirm, Is there a script that would filter gene models at
>> specific AED score.
>> Alternatively if I were to do this within maker with regards to
>> parameters
>> in maker_opts.ctl file I would have to provide my predicted genes gff3
>> file to model_gff and  set AED_threshold at desired threshold?
>>
>> Thanks and regards,
>> Parul Kudtarkar
>>
>>> AED score with 1 are the ones you don't want.  0 is best and 1 is worst
>>> as
>>> it is a distance metric.  You can use the AED_threshold parameter to
>>> require better matching to the evidence by setting it closer to 0. You
>>> can
>>> also try to increase protein homology evidence as some of your calls
>>> may
>>> be split genes due to lack of evidence linking them.
>>>
>>> --Carson
>>>
>>>
>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:
>>>
>>>>Dear Maker community,
>>>>
>>>>For gene-prediction I get training data-set from evidence based
>>>>prediction, I use this data-set to train SNAP as well as Augustus
>>>>predictions, followed by boot-strapping. I would typically expect
>>>> 20-30K
>>>>genes however I am getting 8 times the expected gene count indicating
>>>> too
>>>>many false positives. Is there a way to further refine these
>>>>predication/script to retain predictions with AED score 1 and if yes
>>>> how
>>>>to go about this?
>>>>
>>>>Thanks and regards,
>>>>Parul Kudtarkar
>>>>
>>>>--
>>>>Scientific Programmer
>>>>Center for Computational Regulatory Genomics
>>>>Beckman Institute,
>>>>California Institute of Technology
>>>>http://www.spbase.org
>>>>
>>>>
>>>>_______________________________________________
>>>>maker-devel mailing list
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>>>
>>>
>>>
>>
>>
>> --
>> 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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--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org