designPrimers: Design primers for amplicons
In BIMSBbioinfo/AmpliconBiSeq: analyzing amplicon bisulfite sequencing data

Description Usage Arguments Author(s) See Also

Designs primers for Amplicon Bisulfite sequencing experiments

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designPrimers(target, genome, tag = NULL, primer3 = NULL, settings = NULL,
  thermoParam = NULL, sizeRange = c(151, 500), Tm = c(55, 57, 58),
  ncores = 4)

`target`	`DNAStringSet` or `GRanges` object. If it is a GRanges object you need to provide BSgenome package with it. If it is a `DNAStringSet` object then names argument should contain chromomsome,start and end, by following "chr_start_end" naming convetion.
`genome`	default is NULL, it needs to be set only if target is set to be a `GRanges` object
`tag`	extra information about amplicons, this will be concatanated to the names of BioStringSet object which is either created internally or provided by the user by supplying 'target' argument with a `BioStringSet` object
`primer3`	the filesystem path to primer3 executable, default value NULL will use the version installed with the package
`settings`	text file for p3 settings. Default value NULL will use the default settings file installed with the package.
`termoParam`	Location for thermodynamic parameters for primer3, this should designate a directory, not a single file. Default value NULL, will use the directory that is installed with the package.
`sizeRange`	a two element vector of integers for size range of the amplicons
`Tm`	a three element vector having minimum,optimum and maximum melting tempratures for primer desing (in that order).
`ncores`	number of cores to run on. default=1