[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

[Carson Holt]

Make sure you are training either SNAP or Augustus and not just protein2genome or est2genome. You can also rescue rejected Augustus/SNAP models by running them through InterProScan and then giving any model that contains an InterPro domain to the model_gff= option.

BASIC PROTOCOL 5 from this protocols paper —> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/

—Carson

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