[maker-devel] Re-annotation of a previous annotation with "est2genome=1"

[Eduardo Dupim]

Hi everyone,

I'm trying to annotate a de novo Drosophila genome in MAKER 2.31.9.
Unfortunately, the program annotated few proteins (4081, while flies have
~13K). After some investigation, I think this occurred because I used the
option "est2genome=1", that restrict the final annotation with my
transcriptome file (with ~6K sequences).

I noted that my "all.maker.augustus_masked.proteins.fasta" output have ~12K
genes.

Is it possible to correct this mistake without starting from the begin? I
start a new run with "est2genome=0" and using the previous gff output in
several options, but it seems like it will take forever to finish.

Also, would it be necessary some filtering/edition in the "all.gff file"
when put it in the options like "est_gff" and "rm_gff"?

Thank you,
Eduardo
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