[maker-devel] Maker annotation AED scores are around 0.5

[Carson Holt]

Probably this —>

https://groups.google.com/forum/#!searchin/maker-devel/Curious$20pattern$20in$20AED$20distributions%7Csort:date/maker-devel/QS3VnxhvEks/q3lPmywjBQAJ <https://groups.google.com/forum/#!searchin/maker-devel/Curious$20pattern$20in$20AED$20distributions|sort:date/maker-devel/QS3VnxhvEks/q3lPmywjBQAJ>


Likely caused by an over abundance of single-exon models and under masking of repeats in the genome.

—Carson



> On Mar 30, 2020, at 3:37 AM, Wei Zhao <zhao.wei at umu.se> wrote:
> 
> Dear maker team,
>  
> I am writing to ask for your help.
>  
> I am using make to annotate a big genome ~9 Gbp, I have 3 evidences: 1)  Transcriptome of this species; 2) protein sequence from relative species; 3) Augustus model trained from pasa.
>  
> When I use all of these 3 evidences to annotate the genome (basic pipeline), the distribution of AED score is weird (single peak around 0.5).
>  
> I have also tried to update the gene model I got from pasa  using maker, the distribution of AED scores is the same.
>  
> But when I try to only use  EST or protein as evidence (est2genome or protein2genome), the AED scores is normal (close to 0).
>  
> To my understand, it seems all the 3 evidences are conflict with each other, results in  the AED scores is higher  (~ 0.5) than expected,  could you give me some suggestion on how to fix this problem?
>  
> Best regards,
>  
> Wei
>  
>  
> <E6F3EF742C40408F8390EE9A1FF29894.png>
>  
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