Description Usage Arguments Value Examples
Extract amplicons from sequences from insilicoPCR
object
1 | extract(x)
|
x |
object of class |
object of class DNAStringSet
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ##Run local primer blast
query <- readDNAStringSet("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/010/525/GCA_000010525.1_ASM1052v1/GCA_000010525.1_ASM1052v1_genomic.fna.gz")
primers <- c("GGCTGGATCACCTCCTT","GCCWAGGCATCCDCC")
db <- makeprimerdb(primers)
#Define BLAST arguments: these are the same that can be found in `RinsilicoPCR::blast.params$primers`
args <- list(
outfmt="'6 qacc sacc pident length qlen slen qstart sstart qend send evalue'",
max_target_seqs=20,
word_size=8
)
blastres <- blast(query,db,args)
pairs <- primer.insilico(blastres)
amplicons <- extract(pairs)
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