[maker-devel] Some transcripts have no AED?

[Carson Holt]

Do they have no AED or an AED value of 0. A value of 0 means a perfect match to the evidence.

Also make sure you are not looking for AED in the predictions (i.e. GFF3 source column snap/augustus that are of type match/match_part). Those are rejected models and will not have quality statistics calculated for them (they are only there as alignments for reference purposes).

Only models with the source column of ‘maker’ and a type of 'gene/mRNA/exon/CDS’ represent the gene models and will have AED and QI values.

You can force MAKER to also calculate quality statistics for rejected models by altering pred_stats in the maker_opts.ctl file. 

pred_stats=0 #report AED and QI statistics for all predictions as well as models

—Carson

> On Mar 13, 2018, at 9:53 PM, wangzhennan at ioz.ac.cn wrote:
> 
> Hi,
> 
>    When I used maker to get the AED value, some transcripts have no AED values in the result. Why? I used the RNA-Seq data and protein to run maker.Thank you.
> 
>    Best wishes.
> 
> 
> 
>                                                                                                                                                                Wang
> 
> T
> 
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