[Bioc-sig-seq] question about N

[Martin Morgan]

On 09/07/2011 07:24 PM, wang peter wrote:
> 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?

maybe match(id(qualifiedReads), id(reads)] but it's really hard for me 
to understand your question. Maybe someone else will help.

Martin

>
> 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
>
> 	[[alternative HTML version deleted]]
>
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