[maker-devel] Question about re-annotation

[Thodoris Danis]

Hello maker community,


I am annotating a fish genome with Maker 2.31.10, for which I have transcript evidence and proteins from closely related species. I am running maker in several passes and pass the gff output to the nest pass every time here (
"#-----Re-annotation Using MAKER Derived GFF3
maker_gff= #re-annotate genome based on this gff3 file",
), is this wrong? and where is the difference running the maker from scratch without re-supplying every time the new gff?

Secondly,  in the second round after predictors training, have I to keep est2genome=1 , protein2genome=1, ests and proteins evidence or not?
How do we switch all thesre parameters?

Any input from experienced maker users is welcome
Thank you for your help


Θεόδωρος Δανης
Thodoris Danis
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