[maker-devel] Maker predicts way too few genes/proteins

[Adam Stuckert]

Hello,

I am working on annotating several different assemblies, but I am having
difficulty getting a reasonable number of predicted genes/proteins. My
annotations always predict way too few genes (thousands too few) in the
final transcript/protein fasta files. So, I am seeking help.

My approach is to annotate with EST evidence from the same species (either
straight from transcriptome assemblers or predicted coding regions from
TransDecoder) and use protein evidence from uniprot + related species.
Simple repeats are softmasked within Maker. All repeats are masked in
Maker, and I am supplying a repeat library that includes lineage-specific
repeats as well as species specific repeats that are modeled by
RepeatModeler2. I am using Maker version 3.01.03.

I'm attaching my options control file. Any help to troubleshoot this
would be greatly appreciated.

Thanks,
Adam

-- 
Adam Stuckert
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