outputSeq: Clean up sequence with primers

In mutolisp/seqParser: Parsing DNA sequences (seqParser)

Description

Clean up sequence with primers

Usage

outputSeq(fastaFile, outputFasta, batchName, fprimer, rprimer, duplinum,
  srange, sort = 4)

Arguments

fastaFile	a fasta file path
outputFasta	output fasta file path
fprimer	forward primer
rprimer	reverse primer
duplinum	only select the sequences which duplicate number is greater and equal than 'duplinum'
srange	minimum and maximum values of prunned sequence length, ex: c(20, 150) means the minimum number is 20 and maximum number is 150
sort	sort output table by id (1), pruned sequence (2), duplicates (3) or pruned sequence length (4)

Value

data.table format sequence set

mutolisp/seqParser documentation built on May 23, 2019, 10:52 a.m.