Abinitio annotation looses many genes from EST annotation

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

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




_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

AEDs.png (51K) Download Attachment