dear all:
Using vcountPattern, i found some matched sequences.
but those are not similar to the pattern.
see such coding
rm(list=ls())
reads <- readFastq(fastqfile);#downloaded from
http://biocluster.ucr.edu/~tbackman/query.fastq
seqs <- sread(reads);
PCR2rc<-DNAString("AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA")
result <- vcountPattern(PCR2rc, seqs, max.mismatch=1, min.mismatch=0,
with.indels=TRUE, algorithm="indels")
reads <- reads[result]
seqs <- sread(reads)
sum(result)
then using countPattern, i found they are really not match
subject1 = "GTTGGTGCAAACATTAGTTCTTCTGTTGGTGCAACCTTTG"
result <- countPattern(PCR2rc, subject1, max.mismatch=1, min.mismatch=0,
with.indels=TRUE)
[1] 0
shan gao
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