MAKER3 beta - EVM under predicting

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MAKER3 beta - EVM under predicting

Tuan Duong
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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Re: MAKER3 beta - EVM under predicting

Carson Holt-2
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 <[hidden email]> 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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http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org