Difference between AED=1 and keep_preds=1

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Difference between AED=1 and keep_preds=1

Patrick Tran Van-2

Hi,


From what I understand, an AED of 1 means that the gene predicted by gene finder is not supported by external evidence (transcriptome and protein).


So how is it different with keep_preds=1, which is describe as "add unsupported gene prediction" ?

Because I have way more gene with keep_pred=1.


Maybe I missed something.


Thanks.


Patrick

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Re: Difference between AED=1 and keep_preds=1

Carson Holt-2
keep_preds=1 will take all the raw predictions remove any that overlap the current supported gene set, then filter for redundancy (i.e. if you ran both SNAP and Augustus), then add what’s left to the final gene models. It’s basically the equivalent of taking all the models in the non-overlapping.abiinit file in a normal MAKER run and adding them to the final models.

—Carson


On Dec 1, 2017, at 1:27 PM, Patrick Tran Van <[hidden email]> wrote:

Hi,

From what I understand, an AED of 1 means that the gene predicted by gene finder is not supported by external evidence (transcriptome and protein).

So how is it different with keep_preds=1, which is describe as "add unsupported gene prediction" ?
Because I have way more gene with keep_pred=1. 

Maybe I missed something.

Thanks.

Patrick 


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Re: Difference between AED=1 and keep_preds=1

Patrick Tran Van-2

Ok for keep_preds but AED=1 means no support at all or (very) bad support ?


Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

From: Carson Holt <[hidden email]>
Sent: Friday, December 1, 2017 10:11 PM
To: Patrick Tran Van
Cc: [hidden email]
Subject: Re: Difference between AED=1 and keep_preds=1
 
keep_preds=1 will take all the raw predictions remove any that overlap the current supported gene set, then filter for redundancy (i.e. if you ran both SNAP and Augustus), then add what’s left to the final gene models. It’s basically the equivalent of taking all the models in the non-overlapping.abiinit file in a normal MAKER run and adding them to the final models.

—Carson


On Dec 1, 2017, at 1:27 PM, Patrick Tran Van <[hidden email]> wrote:

Hi,

From what I understand, an AED of 1 means that the gene predicted by gene finder is not supported by external evidence (transcriptome and protein).

So how is it different with keep_preds=1, which is describe as "add unsupported gene prediction" ?
Because I have way more gene with keep_pred=1. 

Maybe I missed something.

Thanks.

Patrick 


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Re: Difference between AED=1 and keep_preds=1

Carson Holt-2
It means no support at all.

—Carson



On Dec 3, 2017, at 3:08 AM, Patrick Tran Van <[hidden email]> wrote:

Ok for keep_preds but AED=1 means no support at all or (very) bad support ?

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

From: Carson Holt <[hidden email]>
Sent: Friday, December 1, 2017 10:11 PM
To: Patrick Tran Van
Cc: [hidden email]
Subject: Re: Difference between AED=1 and keep_preds=1
 
keep_preds=1 will take all the raw predictions remove any that overlap the current supported gene set, then filter for redundancy (i.e. if you ran both SNAP and Augustus), then add what’s left to the final gene models. It’s basically the equivalent of taking all the models in the non-overlapping.abiinit file in a normal MAKER run and adding them to the final models.

—Carson


On Dec 1, 2017, at 1:27 PM, Patrick Tran Van <[hidden email]> wrote:

Hi,

From what I understand, an AED of 1 means that the gene predicted by gene finder is not supported by external evidence (transcriptome and protein).

So how is it different with keep_preds=1, which is describe as "add unsupported gene prediction" ?
Because I have way more gene with keep_pred=1. 

Maybe I missed something.

Thanks.

Patrick 




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