primer.design
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 processors=Autodetect number of available processors and use all available.
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.