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

[Wei Zhao]

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


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