dear members:
i have a question, that is
i remove 5' and 3' N, and do statistics on reads with N in the middle
then, i removed reads with N less than the cutoff
but those remainding reads still contain N
so i must use their id to retrieve original reads, See #1
so what can i do?
part of coding
seqsWithoutNend <-trimLRPatterns(Rpattern = letter_subject, Lpattern =
letter_subject,subject = injectedseqs)
nCount<-alphabetFrequency(seqsWithoutNend)[,"N"]
nDist<- table(nCount)
cutoff=2
filter1 <- nFilter(threshold=cutoff)
qualifiedReads <- reads[filter1(seqsWithoutNend)]
reads[id(qualifiedReads)] #1
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