Abinitio annotation looses many genes from EST annotation

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Abinitio annotation looses many genes from EST annotation

Ricardo Nuno Ferreira Martins Guerreiro

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

  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

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,

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