[maker-devel] AED score

[Parul Kudtarkar]

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