[maker-devel] AED score

[Parul Kudtarkar]

Dear Carson and Daniel,

Thanks. I ran sample file for filtering genes based on AED score. The
input gff3 file was provided to option model_pred(see attached file
Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5
genes with AED score less than 0.75. However there were no genes predicted
in the output file(see attached file Scaffold1_out). I have also attached
the maker_opts.ctl. Could you please advice on this.

Thanks and regards,
Parul Kudtarkar

> Use the AED_threshold option in the maker_opts.ctl file if you just want
> to restrict final gene models to close matches directly within maker.  On
> the other hand, if you are trying to build a dataset for training gene
> predictors, use the maker2zff script for generating a filtered dataset for
> SNAP training.  There are a number of filters available. Just call the
> script once without parameters to see the options.
>
> Thanks,
> Carson
>
>
>
>
> On 12-11-27 5:55 PM, "Daniel Ence" <dence at genetics.utah.edu> wrote:
>
>>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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>>maker-devel mailing list
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>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
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>
>
>
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--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org
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