[maker-devel] Abinitio annotation looses many genes from EST annotation

[Ricardo Nuno Ferreira Martins Guerreiro]

Hello,

It appears to me that my abInitio SNAP + Augustus (trained by nexflow) 
results are worse than the first (est2genome and prot2genome) run. The 
gene number decreases by more than 6000, the opposite of what I 
expected.

  Additionally, my abInitio rerun also has less genes than a previous 
SNAP reannotation.. The AED plots all look more or less the same but the 
number of genes lowers instead of increasing as I expected (image in 
annex).

I'be been running my maker+nextflow pipeline with consistently good 
results, this species is the exception now.

Do you have any suggestion? Should I ditch AbInitio training and use the 
Evidence based annotation? Or maybe just use the closest Augustus model 
instead of training my own?

Kind regards,
Ricardo



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