[maker-devel] MAKER3 beta - EVM under predicting

[Carson Holt]

If ab initio predictors and evidence alignments aren’t in high concordance, then EVM won’t produce results. This often indicates minor sequencing errors in the assembly (this is very common in draft assemblies). Ab initio predictors will slightly alter splicing and extend introns/exons to make a model work around these variations, but doing this does not always concord well with the alignment, so EVM produces nothing. In these cases it is often better just to train the predictor as well as you can, and then take the standard MAKER results.

—Carson





> On Sep 19, 2017, at 11:23 AM, Tuan Duong Anh <tuanduonganh at gmail.com> wrote:
> 
> Dear MAKER-devel group
> 
> I have been testing out MAKER3 beta version and found out that EVM always returns much less number of models. Did any one experience this before? I do expect that EVM will return less models when compare to other, but not to this extend (only 20% of the expected gene models). Any suggestion would be much appreciated.
> 
> ## Number of models obtained by each gene predictors:
> HLIG.all.maker.augustus_masked.proteins.fasta:11224
> HLIG.all.maker.evm.proteins.fasta:1974
> HLIG.all.maker.genemark.proteins.fasta:11352
> HLIG.all.maker.proteins.fasta:13672
> HLIG.all.maker.snap_masked.proteins.fasta:13404
> 
> ## maker_evm.ctl
> #-----Transcript weights
> evmtrans=10 #default weight for source unspecified est/alt_est alignments
> evmtrans:blastn=0 #weight for blastn sourced alignments
> evmtrans:est2genome=10 #weight for est2genome sourced alignments
> evmtrans:tblastx=0 #weight for tblastx sourced alignments
> evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments
> 
> #-----Protein weights
> evmprot=10 #default weight for source unspecified protein alignments
> evmprot:blastx=2 #weight for blastx sourced alignments
> evmprot:protein2genome=10 #weight for protein2genome sourced alignments
> 
> #-----Abinitio Prediction weights
> evmab=10 #default weight for source unspecified ab initio predictions
> evmab:snap=7 #weight for snap sourced predictions
> evmab:augustus=10 #weight for augustus sourced predictions
> evmab:fgenesh=10 #weight for fgenesh sourced predictions
> evmab:genemark=10 #weight for genemark sourced predictions
> 
> 
> Regards,
> Tuan
> 
> 
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