[maker-devel] keep_preds=0 but some gene models have anyway an AED equal to 1.

[Jacques Dainat]

Dear all,

It is not the first time I see that, but I have an annotation launched with the option keeps_pred=0 that contains gene models with AED score equal to 1. As far as I understand, AED score to 1 means there is no evidence support. So it should be purely abinitio without any line of evidence in front of this prediction.
But as it is written in “Michael S-Cambell et al., Genome Annotation and Curation Using MAKER and MAKER-P,  Current Protocols in Bioinformatics, 2014” page 4.11.36 about the the keep_preds option:
"MAKER rejects models that do not have at least some form of evidence support.” Setting keep_preds to 1 “remove the evidence support requirement”.

So, how should I understand my results? Some predictions with low support (but support anyway) can have AED score equal to 1? Or some purely abinitio prediction without support at all can anyway be selected even when keep_preds=0 is set up? 

Best regards,

Jacques Dainat

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