i think remove low quality is better
because the low quality position on the 3' end will lead to many mismatch.
so you could not set the parameter of mismatch well

after remove low quality 3' end, it is easy for good match between 3' end
with adaptor

but i met another problem, when i trimmed the adaptor on the data without
low quality 3' end

the lenght of reads are not uniform, the max is 40
when i use a 40 long adaptor
PCR2<- DNAString("AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAA")
> a<-trimLRPatterns(Rpattern = PCR2, subject = seqs, max.Rmismatch=0.1,
with.Rindels=T)
Error in solveUserSEW(width(x), start = start, end = end, width = width) :
  solving row 2934: 'allow.nonnarrowing' is FALSE and the supplied start (0)
is < 1

i think maybe it is due to many read lenght is below than 40
but when i run this on linux, it is ok

the r version:

sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-mingw32/x64 (64-bit)
sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

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