[maker-devel] Difference between AED=1 and keep_preds=1

[Carson Holt]

It means no support at all.

—Carson



> On Dec 3, 2017, at 3:08 AM, Patrick Tran Van <patrick.tranvan at unil.ch> 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 <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: Friday, December 1, 2017 10:11 PM
> To: Patrick Tran Van
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> 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 <patrick.tranvan at unil.ch <mailto:patrick.tranvan at unil.ch>> 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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