On 09/07/2011 11:34 AM, wang peter wrote:
i replaced the low quality position with "N"
and then trimmed N from 5' and 3'
i got the reads which only contain the "N" in the middle
if i want to find those reads before replacement by "N"
WHAT CAN I DO?
Hi Peter --
Not sure what you mean, probably not this
library(ShortRead)
example(readFastq) ## defines 'rfq' variable
startsWithN <- as.character(narrow(sread(rfq), 1, 1)) == "N"
endsWithN <-
as.character(narrow(sread(rfq), width(rfq), width(rfq))) == "N"
middleN <-
!startsWithN & !endsWithN & alphabetFrequency(sread(rfq))[,"N"] != 0
rfq[!middleN]
I think below your code can be simplified with
at <- as(quality(read), "matrix") < qualityCutoff
Martin
THX
such is coding
library(ShortRead)
reads<- readFastq(fastqfile);#
ids<- id(reads); #
seqs<- sread(reads);
nCount<-alphabetFrequency(seqs)[,"N"]
nDist<- table(nCount)
qualityCutoff<- 20
qual<- PhredQuality(quality(quality(reads)))
myqual_mat<- matrix(charToRaw(as.character(unlist(qual))),
nrow=length(qual), byrow=TRUE) # convert quality score to matrix
at<- myqual_mat<
charToRaw(as.character(PhredQuality(as.integer(qualityCutoff))))
letter_subject<- DNAString(paste(rep.int("N", width(seqs)[1]),
collapse=""))
letter<- as(Views(letter_subject, start=1, end=rowSums(at)),
"DNAStringSet")
injectedseqs<- replaceLetterAt(seqs, at, letter)
trimmed<-trimLRPatterns(Rpattern = letter_subject, Lpattern =
letter_subject,subject = injectedseqs)
nCount<-alphabetFrequency(trimmed)[,"N"]
nDist<- table(nCount)
thank u
shan gao
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