Abinitio annotation looses many genes from EST annotation
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?