[Bioc-sig-seq] remove adaptor before remove barcode

[Harris A. Jaffee]

I'm sorry, but I can't guess what "my method" was, nor what you are  
asking now.
Also, whether you are saying that something works at one end of a  
'subject' but
not the other (so you had to reflect?), and what 'trimmedReads' is.

On Sep 26, 2011, at 10:39 PM, wang peter wrote:

> dear harris:
>         thank you very much for your help, but i think your method  
> can only deal with
> the special case.
>          we need a more general method to remove adaptor and  
> barcode in 3' or 5'
> position.
>          so i write such coding to remove 3' adaptor+barcode
> PCR2<- DNAString 
> ("CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT")
> barcode1 <- DNAString("CGATT")
> PCR2<- append(PCR2,barcode1)
> PCR2rc<-reverseComplement(PCR2)#
> clippedCoords <- trimLRPatterns(Rpattern = PCR2rc, subject = sread 
> (trimmedReads), max.Rmismatch=0.2, with.Rindels=T,ranges=T)
> clippedReads <- narrow(trimmedReads, start=start(clippedCoords),  
> end=end(clippedCoords))
>       but for adaptor on the 5' end
> we must find a more general way to recognize them and remove the  
> whole reads??
>
> shan gao