[maker-devel] AED score

[Parul Kudtarkar]

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