[Bioc-sig-seq] remove adaptor before remove barcode
Harris A. Jaffee
hj at jhu.edu
Tue Sep 27 18:26:07 CEST 2011
I'm sorry, but I can't guess what "my method" was, nor what you are
Also, whether you are saying that something works at one end of a
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'
> so i write such coding to remove 3' adaptor+barcode
> PCR2<- DNAString
> barcode1 <- DNAString("CGATT")
> PCR2<- append(PCR2,barcode1)
> clippedCoords <- trimLRPatterns(Rpattern = PCR2rc, subject = sread
> (trimmedReads), max.Rmismatch=0.2, with.Rindels=T,ranges=T)
> clippedReads <- narrow(trimmedReads, start=start(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
More information about the Bioc-sig-sequencing