[maker-devel] AED score

[Daniel Ence]

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
>>>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


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