callPrimer3: callPrimer3

In SPLINTER: Splice Interpreter of Transcripts

Description

call primer3 for a given set of DNAstringSet object

Usage

callPrimer3(
  seq,
  size_range = "150-500",
  Tm = c(57, 59, 62),
  name = "Primer1",
  primer3 = "primer3-2.3.7/bin/primer3_core",
  thermo.param = "primer3-2.3.7/src/primer3_config/",
  sequence_target = NULL,
  settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt"
)

Arguments

seq	DNAstring object, one DNA string for the given amplicon
size_range	default: '151-500'
Tm	melting temprature parameters default:c(55,57,58)
name	name of the amplicon in chr_start_end format
primer3	primer3 path
thermo.param	thermodynamic parameters folder
sequence_target	If one or more targets is specified then a legal primer pair must flank at least one of them.
settings	text file for parameters

Details

modified to include SEQUENCE_TARGET as an option

Value

data.frame of designed primers and parameters

Author(s)

Altuna Akalin's modified Arnaud Krebs' original function further modified here by Diana Low

Examples

### NOT RUN ###
# primer_results<-callPrimer3(seq='')

SPLINTER documentation built on Nov. 8, 2020, 8:13 p.m.