WebAugustus alternative transcripts option -> which command line option?

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katharina
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WebAugustus alternative transcripts option -> which command line option?

Post by katharina »

Originally posted in the old forum by Simon Perkins on 17.02.2015 - 16:22
Hello,
We are running augustus locally as we have a big dataset to process, so we would like to map the web parameters we were going to use to command line parameters. Everything else can be set, but the "Alternative transcripts: none, few, medium, many", does anybody know which parameters I should set to get this function in the command line version? There is "alternatives from evidence" but I do not have a hints file, and there is "alternatives from sampling" but that would leave just leave two states, true or false, and not the four states that "none, few medium, and many" would suggest.
Kind regards,
Simon
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katharina
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Re: WebAugustus alternative transcripts option -> which command line option?

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by katharina on 18.02.2015 - 11:44

Code: Select all

none: --sample=100 --keep_viterbi=true --alternatives-from-sampling=false
few: --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=2
medium: --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.08 --minmeanexonintronprob=0.4 --maxtracks=3
many: --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.08 --minmeanexonintronprob=0.3 --maxtracks=20
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