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Primer.design

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Revision as of 17:11, 29 March 2018 by Westcott (Talk | contribs) (Revisions)

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The primer.design ..... It creates a *.otu.cons.fasta, *.primer.summary and *.pick.list files.

Default Settings

The list, fasta and otunumber parameters are required.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01)

Options

name

The name option allows you to provide a name file associated with your fasta file.

count

The count option allows you to provide a count file associated with your fasta and list file.

otulabel

The otunumber parameter is used to indicate the OTU you want to use from your list file. It is required.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu10)

length

The length parameter is used to indicate the length of the primer. The default is 18.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01, length=15)

pdiffs

The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01, pdiffs=1)

mintim

The mintm parameter is used to indicate minimum melting temperature. If a primer's melting temperature is below the minimum then it is ignored.

maxtm

The maxtm parameter is used to indicate maximum melting temperature. If a primer's melting temperature is above the maximum then it is ignored.

cutoff

The cutoff parameter allows you set a percentage of sequences that support the base when constructing the consensus sequences for each OTU. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01, cutoff=95)

processors

The processors parameter allows you to indicate the number of processors you want to use. Default=1.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01, processors=2)

label

The label parameter is used to indicate the label you want to use from your list file. If no label is given the first distance is used.

mothur > primer.design(list=final.an.list, fasta=final.fasta, name=final.names, otulabel=Otu01, label=0.03)

Revisions

  • 1.30.0 - First Introduced
  • 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.